Search report summary of file(s):
  - bud1_A_Homemade95kDB_7PTMs.msf
  - bud2_A_Homemade95kDB_7PTMs.msf
  - bud3_A_Homemade95kDB_7PTMs.msf
  - bud1_C_Homemade95kDB_7PTMs.msf
  - bud2_C_Homemade95kDB_7PTMs.msf
  - bud3_C_Homemade95kDB_7PTMs.msf
  - bud1_T_Homemade95kDB_7PTMs.msf
  - bud2_T_Homemade95kDB_7PTMs.msf
  - bud3_T_Homemade95kDB_7PTMs.msf

Created with Discoverer version: 1.4.0.288

================================================================================

Number of filtered/unfiltered result items:
  - 1442/1490 protein group(s)
  - 5420/68576 merged protein(s)
  - 7427/506536 peptide(s)
  - 27036/1207851 PSM(s)
  - 92577/92577 search input(s)

================================================================================

Peptide Grouping Options
  - Show peptide groups: True
  - Group peptides by: Mass and Sequence

Protein Grouping Options
  - Enable protein grouping: True
  - Consider leucine and isoleucine as equal: True
  - Consider only PSMs with confidence at least: Medium
  - Consider only PSMs with delta Cn better than: 0.15
  - Apply strict maximum parsimony principle: True

No filters applied for data reduction

Result filters:
- Peptide Confidence (Minimum confidence: High)
- Protein Score (Search node: Mascot, Score threshold: 50)

================================================================================

Summary of file bud1_A_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud1_A
Search description: -
Search date: 03/13/2020 16:40:21

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud1_A.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  AspN (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Asp-N
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 10961

 - MudPitScoring: True

================================================================================

Processing details:

03/14/2020 01:08 PM	(6):Mascot:	Total search time was 14 h 17 min.
03/14/2020 01:08 PM	(6):Mascot:	Search completed
03/14/2020 01:08 PM	(6):Mascot:	3302 protein(s) + 1212 decoy proteins scored and inserted into result file in 25.7 s.
03/14/2020 01:08 PM	(6):Mascot:	3302 protein(s) scored
03/14/2020 01:07 PM	(6):Mascot:	Search result finalization started.
03/14/2020 01:06 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/14/2020 01:06 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/14/2020 01:06 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/14/2020 01:06 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/14/2020 01:06 PM	(6):Mascot:	Sending 10627 peptide hits (92575 peptides) to result file
03/14/2020 01:06 PM	(6):Mascot:	Sending 10372 decoy peptide hits (90408 peptides) to result file
03/14/2020 01:06 PM	(6):Mascot:	Reading decoy results
03/14/2020 01:06 PM	(6):Mascot:	Start translating results
03/14/2020 01:06 PM	(6):Mascot:	Start mapping modifications
03/14/2020 01:05 PM	(6):Mascot:	Received 4844 proteins from Mascot server
03/14/2020 01:05 PM	(6):Mascot:	Start mapping 4844 proteins
03/14/2020 01:05 PM	(6):Mascot:	Start parsing results
03/14/2020 01:05 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200313/F019487.dat)
03/14/2020 01:04 PM	(6):Mascot:	Mascot Server completed
03/13/2020 10:49 PM	(6):Mascot:	Mascot result on server (filename=../data/20200313/F019487.dat)
03/13/2020 10:48 PM	(6):Mascot:	Start searching 10990 spectra
03/13/2020 10:48 PM	(4):SEQUEST:	Total search time was 4 h 47 min.
03/13/2020 10:48 PM	(4):SEQUEST:	Search completed
03/13/2020 10:48 PM	(4):SEQUEST:	30981 protein(s) + 29106 decoy proteins scored and inserted into result file in 1 min 14 s.
03/13/2020 10:48 PM	(4):SEQUEST:	30981 protein(s) scored
03/13/2020 10:47 PM	(4):SEQUEST:	Search result finalization started.
03/13/2020 10:46 PM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/13/2020 10:46 PM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/13/2020 10:45 PM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/13/2020 10:45 PM	(4):SEQUEST:	Sending 990 decoy peptide hits (9421 peptides) to result file
03/13/2020 10:21 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 10:21 PM	(4):SEQUEST:	Sending 990 peptide hits (9418 peptides) to result file
03/13/2020 09:57 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 10990)
03/13/2020 09:57 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9670 peptides) to result file
03/13/2020 09:33 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 09:33 PM	(4):SEQUEST:	Sending 1000 peptide hits (9652 peptides) to result file
03/13/2020 09:09 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/13/2020 09:09 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9900 peptides) to result file
03/13/2020 08:58 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 08:58 PM	(4):SEQUEST:	Sending 1000 peptide hits (9893 peptides) to result file
03/13/2020 08:48 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/13/2020 08:47 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9896 peptides) to result file
03/13/2020 08:33 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 08:33 PM	(4):SEQUEST:	Sending 1000 peptide hits (9889 peptides) to result file
03/13/2020 08:19 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/13/2020 08:19 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9761 peptides) to result file
03/13/2020 07:36 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 07:36 PM	(4):SEQUEST:	Sending 1000 peptide hits (9751 peptides) to result file
03/13/2020 06:54 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/13/2020 06:54 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9906 peptides) to result file
03/13/2020 06:42 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 06:42 PM	(4):SEQUEST:	Sending 1000 peptide hits (9939 peptides) to result file
03/13/2020 06:31 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/13/2020 06:31 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9879 peptides) to result file
03/13/2020 06:23 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 06:23 PM	(4):SEQUEST:	Sending 1000 peptide hits (9865 peptides) to result file
03/13/2020 06:14 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/13/2020 06:14 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9887 peptides) to result file
03/13/2020 06:09 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 06:09 PM	(4):SEQUEST:	Sending 1000 peptide hits (9897 peptides) to result file
03/13/2020 06:05 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/13/2020 06:04 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9946 peptides) to result file
03/13/2020 06:03 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 06:03 PM	(4):SEQUEST:	Sending 1000 peptide hits (9944 peptides) to result file
03/13/2020 06:01 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/13/2020 06:01 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9936 peptides) to result file
03/13/2020 05:59 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 05:59 PM	(4):SEQUEST:	Sending 1000 peptide hits (9910 peptides) to result file
03/13/2020 05:58 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/13/2020 05:58 PM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/13/2020 05:58 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9928 peptides) to result file
03/13/2020 05:56 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/13/2020 05:56 PM	(4):SEQUEST:	Sending 1000 peptide hits (9924 peptides) to result file
03/13/2020 05:55 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/13/2020 05:55 PM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/13/2020 05:55 PM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/13/2020 05:55 PM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/13/2020 05:55 PM	(4):SEQUEST:	Looking for existing target FASTA index.
03/13/2020 05:55 PM	(1):Spectrum Selector:	Reading from File 1 of 1:bud1_A.raw (12582 spectra total)


================================================================================

Summary of file bud2_A_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud2_A
Search description: -
Search date: 03/13/2020 16:40:26

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud2_A.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  AspN (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Asp-N
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 10154

 - MudPitScoring: True

================================================================================

Processing details:

03/15/2020 12:16 PM	(6):Mascot:	Total search time was 16 h 54 min.
03/15/2020 12:16 PM	(6):Mascot:	Search completed
03/15/2020 12:16 PM	(6):Mascot:	3045 protein(s) + 1093 decoy proteins scored and inserted into result file in 26 s.
03/15/2020 12:15 PM	(6):Mascot:	3045 protein(s) scored
03/15/2020 12:14 PM	(6):Mascot:	Search result finalization started.
03/15/2020 12:14 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/15/2020 12:14 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/15/2020 12:14 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/15/2020 12:14 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/15/2020 12:14 PM	(6):Mascot:	Sending 9895 peptide hits (86971 peptides) to result file
03/15/2020 12:14 PM	(6):Mascot:	Sending 9676 decoy peptide hits (84741 peptides) to result file
03/15/2020 12:14 PM	(6):Mascot:	Reading decoy results
03/15/2020 12:14 PM	(6):Mascot:	Start translating results
03/15/2020 12:14 PM	(6):Mascot:	Start mapping modifications
03/15/2020 12:13 PM	(6):Mascot:	Received 4428 proteins from Mascot server
03/15/2020 12:13 PM	(6):Mascot:	Start mapping 4428 proteins
03/15/2020 12:13 PM	(6):Mascot:	Start parsing results
03/15/2020 12:13 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200314/F019489.dat)
03/15/2020 12:12 PM	(6):Mascot:	Mascot Server completed
03/14/2020 07:20 PM	(6):Mascot:	Mascot result on server (filename=../data/20200314/F019489.dat)
03/14/2020 07:20 PM	(6):Mascot:	Start searching 10174 spectra
03/14/2020 07:20 PM	(4):SEQUEST:	Total search time was 5 h 14 min.
03/14/2020 07:20 PM	(4):SEQUEST:	Search completed
03/14/2020 07:20 PM	(4):SEQUEST:	30116 protein(s) + 28656 decoy proteins scored and inserted into result file in 1 min 8 s.
03/14/2020 07:20 PM	(4):SEQUEST:	30116 protein(s) scored
03/14/2020 07:18 PM	(4):SEQUEST:	Search result finalization started.
03/14/2020 07:18 PM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/14/2020 07:17 PM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/14/2020 07:17 PM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/14/2020 07:17 PM	(4):SEQUEST:	Sending 174 decoy peptide hits (1602 peptides) to result file
03/14/2020 07:16 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 07:16 PM	(4):SEQUEST:	Sending 174 peptide hits (1600 peptides) to result file
03/14/2020 07:14 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 10174)
03/14/2020 07:14 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9759 peptides) to result file
03/14/2020 06:58 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 06:58 PM	(4):SEQUEST:	Sending 1000 peptide hits (9753 peptides) to result file
03/14/2020 06:42 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/14/2020 06:42 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9667 peptides) to result file
03/14/2020 06:17 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 06:17 PM	(4):SEQUEST:	Sending 1000 peptide hits (9663 peptides) to result file
03/14/2020 05:53 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/14/2020 05:53 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9893 peptides) to result file
03/14/2020 05:39 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 05:38 PM	(4):SEQUEST:	Sending 1000 peptide hits (9890 peptides) to result file
03/14/2020 05:24 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/14/2020 05:24 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9812 peptides) to result file
03/14/2020 05:00 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 05:00 PM	(4):SEQUEST:	Sending 1000 peptide hits (9795 peptides) to result file
03/14/2020 04:37 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/14/2020 04:36 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9659 peptides) to result file
03/14/2020 03:41 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 03:41 PM	(4):SEQUEST:	Sending 1000 peptide hits (9672 peptides) to result file
03/14/2020 02:45 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/14/2020 02:45 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9925 peptides) to result file
03/14/2020 02:35 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 02:35 PM	(4):SEQUEST:	Sending 1000 peptide hits (9918 peptides) to result file
03/14/2020 02:26 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/14/2020 02:25 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9811 peptides) to result file
03/14/2020 02:17 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 02:17 PM	(4):SEQUEST:	Sending 1000 peptide hits (9813 peptides) to result file
03/14/2020 02:10 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/14/2020 02:09 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9986 peptides) to result file
03/14/2020 02:07 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 02:07 PM	(4):SEQUEST:	Sending 1000 peptide hits (9978 peptides) to result file
03/14/2020 02:05 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/14/2020 02:05 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9934 peptides) to result file
03/14/2020 02:04 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 02:04 PM	(4):SEQUEST:	Sending 1000 peptide hits (9925 peptides) to result file
03/14/2020 02:03 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/14/2020 02:02 PM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/14/2020 02:02 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9912 peptides) to result file
03/14/2020 02:01 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/14/2020 02:01 PM	(4):SEQUEST:	Sending 1000 peptide hits (9889 peptides) to result file
03/14/2020 02:00 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/14/2020 02:00 PM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/14/2020 02:00 PM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/14/2020 02:00 PM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/14/2020 02:00 PM	(4):SEQUEST:	Looking for existing target FASTA index.
03/14/2020 02:00 PM	(1):Spectrum Selector:	Reading from File 1 of 1:bud2_A.raw (11820 spectra total)


================================================================================

Summary of file bud3_A_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud3_A
Search description: -
Search date: 03/13/2020 16:40:31

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud3_A.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  AspN (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Asp-N
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 10040

 - MudPitScoring: True

================================================================================

Processing details:

03/16/2020 02:50 PM	(6):Mascot:	Total search time was 19 h 24 min.
03/16/2020 02:50 PM	(6):Mascot:	Search completed
03/16/2020 02:50 PM	(6):Mascot:	2843 protein(s) + 1040 decoy proteins scored and inserted into result file in 26.5 s.
03/16/2020 02:50 PM	(6):Mascot:	2843 protein(s) scored
03/16/2020 02:49 PM	(6):Mascot:	Search result finalization started.
03/16/2020 02:49 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/16/2020 02:49 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/16/2020 02:48 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/16/2020 02:48 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/16/2020 02:48 PM	(6):Mascot:	Sending 9747 peptide hits (85834 peptides) to result file
03/16/2020 02:48 PM	(6):Mascot:	Sending 9547 decoy peptide hits (83656 peptides) to result file
03/16/2020 02:48 PM	(6):Mascot:	Reading decoy results
03/16/2020 02:48 PM	(6):Mascot:	Start translating results
03/16/2020 02:48 PM	(6):Mascot:	Start mapping modifications
03/16/2020 02:48 PM	(6):Mascot:	Received 4360 proteins from Mascot server
03/16/2020 02:48 PM	(6):Mascot:	Start mapping 4360 proteins
03/16/2020 02:47 PM	(6):Mascot:	Start parsing results
03/16/2020 02:47 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200315/F019491.dat)
03/16/2020 02:47 PM	(6):Mascot:	Mascot Server completed
03/15/2020 07:24 PM	(6):Mascot:	Mascot result on server (filename=../data/20200315/F019491.dat)
03/15/2020 07:24 PM	(6):Mascot:	Start searching 10079 spectra
03/15/2020 07:24 PM	(4):SEQUEST:	Total search time was 5 h 56 min.
03/15/2020 07:24 PM	(4):SEQUEST:	Search completed
03/15/2020 07:24 PM	(4):SEQUEST:	29798 protein(s) + 28350 decoy proteins scored and inserted into result file in 1 min 6 s.
03/15/2020 07:24 PM	(4):SEQUEST:	29798 protein(s) scored
03/15/2020 07:23 PM	(4):SEQUEST:	Search result finalization started.
03/15/2020 07:22 PM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/15/2020 07:22 PM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/15/2020 07:21 PM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/15/2020 07:21 PM	(4):SEQUEST:	Sending 79 decoy peptide hits (631 peptides) to result file
03/15/2020 07:20 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 07:20 PM	(4):SEQUEST:	Sending 79 peptide hits (630 peptides) to result file
03/15/2020 07:19 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 10079)
03/15/2020 07:19 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9531 peptides) to result file
03/15/2020 06:54 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 06:54 PM	(4):SEQUEST:	Sending 1000 peptide hits (9512 peptides) to result file
03/15/2020 06:29 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/15/2020 06:28 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9562 peptides) to result file
03/15/2020 05:53 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 05:53 PM	(4):SEQUEST:	Sending 1000 peptide hits (9579 peptides) to result file
03/15/2020 05:18 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/15/2020 05:17 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9847 peptides) to result file
03/15/2020 05:00 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 05:00 PM	(4):SEQUEST:	Sending 1000 peptide hits (9862 peptides) to result file
03/15/2020 04:42 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/15/2020 04:42 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9875 peptides) to result file
03/15/2020 04:28 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 04:28 PM	(4):SEQUEST:	Sending 1000 peptide hits (9893 peptides) to result file
03/15/2020 04:13 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/15/2020 04:13 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9573 peptides) to result file
03/15/2020 03:10 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 03:10 PM	(4):SEQUEST:	Sending 1000 peptide hits (9585 peptides) to result file
03/15/2020 02:06 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/15/2020 02:05 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9919 peptides) to result file
03/15/2020 01:56 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 01:56 PM	(4):SEQUEST:	Sending 1000 peptide hits (9922 peptides) to result file
03/15/2020 01:46 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/15/2020 01:46 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9845 peptides) to result file
03/15/2020 01:40 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 01:40 PM	(4):SEQUEST:	Sending 1000 peptide hits (9850 peptides) to result file
03/15/2020 01:33 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/15/2020 01:33 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9981 peptides) to result file
03/15/2020 01:31 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 01:31 PM	(4):SEQUEST:	Sending 1000 peptide hits (9987 peptides) to result file
03/15/2020 01:28 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/15/2020 01:28 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9925 peptides) to result file
03/15/2020 01:27 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 01:27 PM	(4):SEQUEST:	Sending 1000 peptide hits (9907 peptides) to result file
03/15/2020 01:25 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/15/2020 01:25 PM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/15/2020 01:25 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9919 peptides) to result file
03/15/2020 01:24 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/15/2020 01:24 PM	(4):SEQUEST:	Sending 1000 peptide hits (9915 peptides) to result file
03/15/2020 01:23 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/15/2020 01:23 PM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/15/2020 01:23 PM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/15/2020 01:23 PM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/15/2020 01:23 PM	(4):SEQUEST:	Looking for existing target FASTA index.
03/15/2020 01:22 PM	(1):Spectrum Selector:	Reading from File 1 of 1:bud3_A.raw (11686 spectra total)


================================================================================

Summary of file bud1_C_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud1_C
Search description: -
Search date: 03/13/2020 16:43:27

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud1_C.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Chymotrypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Chymotrypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 9536

 - MudPitScoring: True

================================================================================

Processing details:

03/16/2020 11:21 PM	(6):Mascot:	Total search time was 5 h 31 min.
03/16/2020 11:21 PM	(6):Mascot:	Search completed
03/16/2020 11:21 PM	(6):Mascot:	3185 protein(s) + 1961 decoy proteins scored and inserted into result file in 23.2 s.
03/16/2020 11:21 PM	(6):Mascot:	3185 protein(s) scored
03/16/2020 11:20 PM	(6):Mascot:	Search result finalization started.
03/16/2020 11:20 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/16/2020 11:20 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/16/2020 11:19 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/16/2020 11:19 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/16/2020 11:19 PM	(6):Mascot:	Sending 9359 peptide hits (90518 peptides) to result file
03/16/2020 11:19 PM	(6):Mascot:	Sending 9350 decoy peptide hits (90401 peptides) to result file
03/16/2020 11:19 PM	(6):Mascot:	Reading decoy results
03/16/2020 11:19 PM	(6):Mascot:	Start translating results
03/16/2020 11:19 PM	(6):Mascot:	Start mapping modifications
03/16/2020 11:19 PM	(6):Mascot:	Received 5225 proteins from Mascot server
03/16/2020 11:19 PM	(6):Mascot:	Start mapping 5225 proteins
03/16/2020 11:18 PM	(6):Mascot:	Start parsing results
03/16/2020 11:18 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200316/F019492.dat)
03/16/2020 11:18 PM	(6):Mascot:	Mascot Server completed
03/16/2020 05:48 PM	(6):Mascot:	Mascot result on server (filename=../data/20200316/F019492.dat)
03/16/2020 05:48 PM	(6):Mascot:	Start searching 9538 spectra
03/16/2020 05:48 PM	(4):SEQUEST:	Total search time was 2 h 53 min.
03/16/2020 05:48 PM	(4):SEQUEST:	Search completed
03/16/2020 05:48 PM	(4):SEQUEST:	34003 protein(s) + 32955 decoy proteins scored and inserted into result file in 1 min 4 s.
03/16/2020 05:48 PM	(4):SEQUEST:	34003 protein(s) scored
03/16/2020 05:47 PM	(4):SEQUEST:	Search result finalization started.
03/16/2020 05:46 PM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/16/2020 05:46 PM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/16/2020 05:46 PM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/16/2020 05:46 PM	(4):SEQUEST:	Sending 538 decoy peptide hits (4796 peptides) to result file
03/16/2020 05:16 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 05:16 PM	(4):SEQUEST:	Sending 538 peptide hits (4825 peptides) to result file
03/16/2020 04:44 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 9538)
03/16/2020 04:44 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9605 peptides) to result file
03/16/2020 04:24 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 04:24 PM	(4):SEQUEST:	Sending 1000 peptide hits (9605 peptides) to result file
03/16/2020 04:04 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/16/2020 04:03 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 04:01 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 04:01 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:59 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/16/2020 03:59 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 03:57 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:57 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:54 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/16/2020 03:54 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 03:51 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:51 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:49 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/16/2020 03:49 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 03:46 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:46 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:43 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/16/2020 03:43 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 03:41 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:41 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:38 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/16/2020 03:38 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9991 peptides) to result file
03/16/2020 03:36 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:36 PM	(4):SEQUEST:	Sending 1000 peptide hits (9990 peptides) to result file
03/16/2020 03:33 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/16/2020 03:33 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/16/2020 03:31 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:31 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:29 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/16/2020 03:29 PM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/16/2020 03:29 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9993 peptides) to result file
03/16/2020 03:26 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/16/2020 03:26 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/16/2020 03:23 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/16/2020 03:23 PM	(4):SEQUEST:	FASTA indexing completed in 15 min 36 s.
03/16/2020 03:07 PM	(4):SEQUEST:	Building new decoy FASTA index. This may take up to several hours...
03/16/2020 03:07 PM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/16/2020 03:07 PM	(4):SEQUEST:	FASTA indexing completed in 16 min 26 s.
03/16/2020 02:51 PM	(4):SEQUEST:	Building new target FASTA index. This may take up to several hours...
03/16/2020 02:51 PM	(4):SEQUEST:	Looking for existing target FASTA index.
03/16/2020 02:50 PM	(1):Spectrum Selector:	Reading from File 1 of 1:bud1_C.raw (11345 spectra total)


================================================================================

Summary of file bud2_C_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud2_C
Search description: -
Search date: 03/13/2020 16:43:45

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud2_C.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Chymotrypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Chymotrypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 8458

 - MudPitScoring: True

================================================================================

Processing details:

03/17/2020 07:33 AM	(6):Mascot:	Total search time was 3 h 43 min.
03/17/2020 07:33 AM	(6):Mascot:	Search completed
03/17/2020 07:33 AM	(6):Mascot:	2955 protein(s) + 1888 decoy proteins scored and inserted into result file in 21.3 s.
03/17/2020 07:33 AM	(6):Mascot:	2955 protein(s) scored
03/17/2020 07:32 AM	(6):Mascot:	Search result finalization started.
03/17/2020 07:32 AM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/17/2020 07:32 AM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/17/2020 07:32 AM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/17/2020 07:32 AM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/17/2020 07:32 AM	(6):Mascot:	Sending 8387 peptide hits (81841 peptides) to result file
03/17/2020 07:32 AM	(6):Mascot:	Sending 8375 decoy peptide hits (81814 peptides) to result file
03/17/2020 07:32 AM	(6):Mascot:	Reading decoy results
03/17/2020 07:32 AM	(6):Mascot:	Start translating results
03/17/2020 07:32 AM	(6):Mascot:	Start mapping modifications
03/17/2020 07:31 AM	(6):Mascot:	Received 4883 proteins from Mascot server
03/17/2020 07:31 AM	(6):Mascot:	Start mapping 4883 proteins
03/17/2020 07:31 AM	(6):Mascot:	Start parsing results
03/17/2020 07:31 AM	(6):Mascot:	Received Mascot result file (filename=../data/20200317/F019494.dat)
03/17/2020 07:31 AM	(6):Mascot:	Mascot Server completed
03/17/2020 03:48 AM	(6):Mascot:	Mascot result on server (filename=../data/20200317/F019494.dat)
03/17/2020 03:48 AM	(6):Mascot:	Start searching 8458 spectra
03/17/2020 03:48 AM	(4):SEQUEST:	Total search time was 1 h 31 min.
03/17/2020 03:48 AM	(4):SEQUEST:	Search completed
03/17/2020 03:48 AM	(4):SEQUEST:	32662 protein(s) + 32164 decoy proteins scored and inserted into result file in 53.9 s.
03/17/2020 03:48 AM	(4):SEQUEST:	32662 protein(s) scored
03/17/2020 03:47 AM	(4):SEQUEST:	Search result finalization started.
03/17/2020 03:47 AM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/17/2020 03:46 AM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/17/2020 03:46 AM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/17/2020 03:46 AM	(4):SEQUEST:	Sending 458 decoy peptide hits (4167 peptides) to result file
03/17/2020 03:32 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 03:32 AM	(4):SEQUEST:	Sending 458 peptide hits (4157 peptides) to result file
03/17/2020 03:19 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 8458)
03/17/2020 03:18 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9849 peptides) to result file
03/17/2020 03:09 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 03:09 AM	(4):SEQUEST:	Sending 1000 peptide hits (9852 peptides) to result file
03/17/2020 02:59 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/17/2020 02:59 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:56 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:56 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:54 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/17/2020 02:53 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:50 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:50 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:46 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/17/2020 02:46 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:42 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:42 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:38 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/17/2020 02:38 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:33 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:33 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:29 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/17/2020 02:29 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:26 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:26 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:24 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/17/2020 02:24 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 02:21 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:21 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 02:19 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/17/2020 02:19 AM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/17/2020 02:19 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9990 peptides) to result file
03/17/2020 02:16 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 02:16 AM	(4):SEQUEST:	Sending 1000 peptide hits (9990 peptides) to result file
03/17/2020 02:13 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/17/2020 02:13 AM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/17/2020 02:13 AM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/17/2020 02:13 AM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/17/2020 02:13 AM	(4):SEQUEST:	Looking for existing target FASTA index.
03/17/2020 02:12 AM	(1):Spectrum Selector:	Reading from File 1 of 1:bud2_C.raw (10391 spectra total)


================================================================================

Summary of file bud3_C_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud3_C
Search description: -
Search date: 03/13/2020 16:45:04

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud3_C_1.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Chymotrypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Chymotrypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 9596

 - MudPitScoring: True

================================================================================

Processing details:

03/17/2020 02:32 PM	(6):Mascot:	Total search time was 3 h 25 min.
03/17/2020 02:32 PM	(6):Mascot:	Search completed
03/17/2020 02:32 PM	(6):Mascot:	2900 protein(s) + 1808 decoy proteins scored and inserted into result file in 23.2 s.
03/17/2020 02:32 PM	(6):Mascot:	2900 protein(s) scored
03/17/2020 02:31 PM	(6):Mascot:	Search result finalization started.
03/17/2020 02:31 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/17/2020 02:30 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/17/2020 02:30 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/17/2020 02:30 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/17/2020 02:30 PM	(6):Mascot:	Sending 9534 peptide hits (93169 peptides) to result file
03/17/2020 02:30 PM	(6):Mascot:	Sending 9529 decoy peptide hits (93097 peptides) to result file
03/17/2020 02:30 PM	(6):Mascot:	Reading decoy results
03/17/2020 02:30 PM	(6):Mascot:	Start translating results
03/17/2020 02:30 PM	(6):Mascot:	Start mapping modifications
03/17/2020 02:30 PM	(6):Mascot:	Received 4826 proteins from Mascot server
03/17/2020 02:30 PM	(6):Mascot:	Start mapping 4826 proteins
03/17/2020 02:29 PM	(6):Mascot:	Start parsing results
03/17/2020 02:29 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200317/F019496.dat)
03/17/2020 02:29 PM	(6):Mascot:	Mascot Server completed
03/17/2020 11:05 AM	(6):Mascot:	Mascot result on server (filename=../data/20200317/F019496.dat)
03/17/2020 11:05 AM	(6):Mascot:	Start searching 9597 spectra
03/17/2020 11:05 AM	(4):SEQUEST:	Total search time was 1 h 57 min.
03/17/2020 11:05 AM	(4):SEQUEST:	Search completed
03/17/2020 11:05 AM	(4):SEQUEST:	35352 protein(s) + 34345 decoy proteins scored and inserted into result file in 1 min 9 s.
03/17/2020 11:05 AM	(4):SEQUEST:	35352 protein(s) scored
03/17/2020 11:04 AM	(4):SEQUEST:	Search result finalization started.
03/17/2020 11:03 AM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/17/2020 11:03 AM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/17/2020 11:03 AM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/17/2020 11:03 AM	(4):SEQUEST:	Sending 597 decoy peptide hits (5582 peptides) to result file
03/17/2020 10:41 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 10:41 AM	(4):SEQUEST:	Sending 597 peptide hits (5608 peptides) to result file
03/17/2020 10:19 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 9597)
03/17/2020 10:18 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9972 peptides) to result file
03/17/2020 10:14 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 10:14 AM	(4):SEQUEST:	Sending 1000 peptide hits (9974 peptides) to result file
03/17/2020 10:09 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/17/2020 10:09 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 10:04 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 10:04 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 10:00 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/17/2020 09:59 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:53 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:53 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:46 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/17/2020 09:46 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:42 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:42 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:38 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/17/2020 09:38 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:32 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:32 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:27 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/17/2020 09:27 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:24 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:24 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:21 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/17/2020 09:21 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:18 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:18 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:15 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/17/2020 09:15 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:13 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:13 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:11 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/17/2020 09:11 AM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/17/2020 09:11 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/17/2020 09:07 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/17/2020 09:07 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/17/2020 09:03 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/17/2020 09:03 AM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/17/2020 09:03 AM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/17/2020 09:03 AM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/17/2020 09:03 AM	(4):SEQUEST:	Looking for existing target FASTA index.
03/17/2020 09:03 AM	(1):Spectrum Selector:	Reading from File 1 of 1:bud3_C.raw (11562 spectra total)


================================================================================

Summary of file bud1_T_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud1_T
Search description: -
Search date: 03/20/2020 18:05:15

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud1_T.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Trypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Trypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 11828

 - MudPitScoring: True

================================================================================

Processing details:

03/21/2020 11:41 AM	(6):Mascot:	Total search time was 6 h 22 min.
03/21/2020 11:41 AM	(6):Mascot:	Search completed
03/21/2020 11:41 AM	(6):Mascot:	6015 protein(s) + 3653 decoy proteins scored and inserted into result file in 33.3 s.
03/21/2020 11:41 AM	(6):Mascot:	6015 protein(s) scored
03/21/2020 11:40 AM	(6):Mascot:	Search result finalization started.
03/21/2020 11:40 AM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/21/2020 11:40 AM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/21/2020 11:39 AM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/21/2020 11:39 AM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/21/2020 11:39 AM	(6):Mascot:	Sending 11805 peptide hits (116575 peptides) to result file
03/21/2020 11:39 AM	(6):Mascot:	Sending 11794 decoy peptide hits (116226 peptides) to result file
03/21/2020 11:39 AM	(6):Mascot:	Reading decoy results
03/21/2020 11:39 AM	(6):Mascot:	Start translating results
03/21/2020 11:39 AM	(6):Mascot:	Start mapping modifications
03/21/2020 11:38 AM	(6):Mascot:	Received 8990 proteins from Mascot server
03/21/2020 11:38 AM	(6):Mascot:	Start mapping 8990 proteins
03/21/2020 11:37 AM	(6):Mascot:	Start parsing results
03/21/2020 11:37 AM	(6):Mascot:	Received Mascot result file (filename=../data/20200321/F019500.dat)
03/21/2020 11:37 AM	(6):Mascot:	Mascot Server completed
03/21/2020 05:18 AM	(6):Mascot:	Mascot result on server (filename=../data/20200321/F019500.dat)
03/21/2020 05:18 AM	(6):Mascot:	Start searching 11828 spectra
03/21/2020 05:18 AM	(4):SEQUEST:	Total search time was 2 h 50 min.
03/21/2020 05:18 AM	(4):SEQUEST:	Search completed
03/21/2020 05:18 AM	(4):SEQUEST:	40633 protein(s) + 39074 decoy proteins scored and inserted into result file in 1 min 30 s.
03/21/2020 05:17 AM	(4):SEQUEST:	40633 protein(s) scored
03/21/2020 05:15 AM	(4):SEQUEST:	Search result finalization started.
03/21/2020 05:15 AM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/21/2020 05:15 AM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/21/2020 05:14 AM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/21/2020 05:14 AM	(4):SEQUEST:	Sending 828 decoy peptide hits (8201 peptides) to result file
03/21/2020 05:03 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:03 AM	(4):SEQUEST:	Sending 828 peptide hits (8208 peptides) to result file
03/21/2020 04:52 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 11000 - 11828)
03/21/2020 04:52 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9901 peptides) to result file
03/21/2020 04:28 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 04:28 AM	(4):SEQUEST:	Sending 1000 peptide hits (9892 peptides) to result file
03/21/2020 04:04 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 11000)
03/21/2020 04:04 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 03:45 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 03:45 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 03:26 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/21/2020 03:26 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 03:13 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 03:13 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 03:00 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/21/2020 03:00 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:54 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:54 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:49 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/21/2020 02:49 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:45 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:45 AM	(4):SEQUEST:	Sending 1000 peptide hits (9982 peptides) to result file
03/21/2020 02:41 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/21/2020 02:40 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:38 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:38 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:35 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/21/2020 02:35 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:33 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:33 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:31 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/21/2020 02:31 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:30 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:30 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:28 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/21/2020 02:28 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:27 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:27 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:26 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/21/2020 02:26 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:25 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:25 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:24 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/21/2020 02:24 AM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/21/2020 02:24 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 02:23 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 02:23 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 02:21 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/21/2020 02:21 AM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/21/2020 02:21 AM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/21/2020 02:21 AM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/21/2020 02:21 AM	(4):SEQUEST:	Looking for existing target FASTA index.
03/21/2020 02:21 AM	(1):Spectrum Selector:	Reading from File 1 of 1:bud1_T.raw (13423 spectra total)


================================================================================

Summary of file bud2_T_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud2_T
Search description: -
Search date: 03/20/2020 18:05:24

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud2_T.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Trypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Trypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 11242

 - MudPitScoring: True

================================================================================

Processing details:

03/21/2020 10:19 PM	(6):Mascot:	Total search time was 3 h 30 min.
03/21/2020 10:19 PM	(6):Mascot:	Search completed
03/21/2020 10:19 PM	(6):Mascot:	4697 protein(s) + 2800 decoy proteins scored and inserted into result file in 30.9 s.
03/21/2020 10:18 PM	(6):Mascot:	4697 protein(s) scored
03/21/2020 10:17 PM	(6):Mascot:	Search result finalization started.
03/21/2020 10:17 PM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/21/2020 10:17 PM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/21/2020 10:17 PM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/21/2020 10:17 PM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/21/2020 10:17 PM	(6):Mascot:	Sending 11212 peptide hits (110372 peptides) to result file
03/21/2020 10:16 PM	(6):Mascot:	Sending 11195 decoy peptide hits (110090 peptides) to result file
03/21/2020 10:16 PM	(6):Mascot:	Reading decoy results
03/21/2020 10:16 PM	(6):Mascot:	Start translating results
03/21/2020 10:16 PM	(6):Mascot:	Start mapping modifications
03/21/2020 10:16 PM	(6):Mascot:	Received 7041 proteins from Mascot server
03/21/2020 10:16 PM	(6):Mascot:	Start mapping 7041 proteins
03/21/2020 10:15 PM	(6):Mascot:	Start parsing results
03/21/2020 10:15 PM	(6):Mascot:	Received Mascot result file (filename=../data/20200321/F019502.dat)
03/21/2020 10:15 PM	(6):Mascot:	Mascot Server completed
03/21/2020 06:46 PM	(6):Mascot:	Mascot result on server (filename=../data/20200321/F019502.dat)
03/21/2020 06:46 PM	(6):Mascot:	Start searching 11242 spectra
03/21/2020 06:46 PM	(4):SEQUEST:	Total search time was 1 h 49 min.
03/21/2020 06:46 PM	(4):SEQUEST:	Search completed
03/21/2020 06:46 PM	(4):SEQUEST:	39058 protein(s) + 37474 decoy proteins scored and inserted into result file in 1 min 25 s.
03/21/2020 06:45 PM	(4):SEQUEST:	39058 protein(s) scored
03/21/2020 06:44 PM	(4):SEQUEST:	Search result finalization started.
03/21/2020 06:43 PM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/21/2020 06:43 PM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/21/2020 06:43 PM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/21/2020 06:43 PM	(4):SEQUEST:	Sending 242 decoy peptide hits (2310 peptides) to result file
03/21/2020 06:41 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 06:41 PM	(4):SEQUEST:	Sending 242 peptide hits (2303 peptides) to result file
03/21/2020 06:39 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 11000 - 11242)
03/21/2020 06:39 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9978 peptides) to result file
03/21/2020 06:27 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 06:27 PM	(4):SEQUEST:	Sending 1000 peptide hits (9980 peptides) to result file
03/21/2020 06:15 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 11000)
03/21/2020 06:14 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9971 peptides) to result file
03/21/2020 06:04 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 06:04 PM	(4):SEQUEST:	Sending 1000 peptide hits (9970 peptides) to result file
03/21/2020 05:54 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/21/2020 05:54 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 05:43 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:43 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 05:32 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/21/2020 05:32 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 05:26 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:26 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 05:19 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/21/2020 05:19 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 05:15 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:15 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 05:10 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/21/2020 05:10 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 05:07 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:07 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 05:04 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/21/2020 05:04 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 05:02 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 05:02 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 05:00 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/21/2020 05:00 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 04:59 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 04:59 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 04:57 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/21/2020 04:57 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 04:56 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 04:56 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 04:55 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/21/2020 04:55 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/21/2020 04:54 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 04:54 PM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/21/2020 04:53 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/21/2020 04:53 PM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/21/2020 04:53 PM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9999 peptides) to result file
03/21/2020 04:52 PM	(4):SEQUEST:	Starting SEQUEST decoy search
03/21/2020 04:52 PM	(4):SEQUEST:	Sending 1000 peptide hits (9995 peptides) to result file
03/21/2020 04:51 PM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/21/2020 04:51 PM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/21/2020 04:51 PM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/21/2020 04:51 PM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/21/2020 04:51 PM	(4):SEQUEST:	Looking for existing target FASTA index.
03/21/2020 04:50 PM	(1):Spectrum Selector:	Reading from File 1 of 1:bud2_T.raw (12858 spectra total)


================================================================================

Summary of file bud3_T_Homemade95kDB_7PTMs.msf

Workflow created with Discoverer version: 1.4.0.288 (DBVersion:79)

================================================================================

Search name: bud3_T
Search description: -
Search date: 03/20/2020 18:05:33

================================================================================

The pipeline tree:
------------------

  |-(0) Spectrum Files
    |-(1) Spectrum Selector
      |-(4) SEQUEST
        |-(5) Target Decoy PSM Validator
      |-(6) Mascot
        |-(7) Target Decoy PSM Validator


------------------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------------------

Input Data:
-----------------------------
File Name(s):  bud3_T.raw

------------------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------------------

1. General Settings:
-----------------------------
Precursor Selection:  Use MS1 Precursor
Use New Precursor Reevaluation:  True

2. Spectrum Properties Filter:
-----------------------------
Lower RT Limit:  0
Upper RT Limit:  0
First Scan:  0
Last Scan:  0
Lowest Charge State:  2
Highest Charge State:  20
Min. Precursor Mass:  300 Da
Max. Precursor Mass:  10000 Da
Total Intensity Threshold:  0
Minimum Peak Count:  1

3. Scan Event Filters:
-----------------------------
Mass Analyzer:  Is ITMS
MS Order:  Is MS2
Activation Type:  Is CID
Min. Collision Energy:  5
Max. Collision Energy:  60
Scan Type:  Is Full
Ionization Source:  Is Nanospray
Polarity Mode:  Is +

4. Peak Filters:
-----------------------------
S/N Threshold (FT-only):  1.5

5. Replacements for Unrecognized Properties:
-----------------------------
Unrecognized Charge Replacements:  Automatic
Unrecognized Mass Analyzer Replacements:  ITMS
Unrecognized MS Order Replacements:  MS2
Unrecognized Activation Type Replacements:  CID
Unrecognized Polarity Replacements:  +

6. Just for Testing:
-----------------------------
Precursor Clipping Range Before:  2.5 Da
Precursor Clipping Range After:  5.5 Da

------------------------------------------------------------------------------
Processing node 4: SEQUEST
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar.fasta
Enzyme Name:  Trypsin (Full)
Maximum Missed Cleavage Sites:  12

1.1 Peptide Scoring Options:
-----------------------------
Maximum Peptides Considered:  500
Maximum Peptides Output:  10
Calculate Probability Scores:  False
Absolute XCorr Threshold:  0.4
Fragment Ion Cutoff Percentage:  0.1
Peptide Without Protein XCorr Threshold:  1.5

1.2 Protein Scoring Options:
-----------------------------
Maximum Protein References Per Peptide:  100
Protein Relevance Threshold:  1.5
Peptide Relevance Factor:  0.4

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False
Use Average Fragment Masses:  False

3. Ion Series:
-----------------------------
Use Neutral Loss a Ions:  True
Use Neutral Loss b Ions:  True
Use Neutral Loss y Ions:  True
Weight of a Ions:  0
Weight of b Ions:  1
Weight of c Ions:  0
Weight of x Ions:  0
Weight of y Ions:  1
Weight of z Ions:  0

4. Dynamic Modifications:
-----------------------------
Max. Modifications Per Peptide:  4
N-Terminal Modification:  Acetyl / +42.011 Da (Any N-Terminus)
1. Dynamic Modification:  Oxidation / +15.995 Da (M)
2. Dynamic Modification:  N-acetyl-D-glucosamine / +221.090 Da (N)
3. Dynamic Modification:  Methyl / +14.016 Da (K)
4. Dynamic Modification:  Acetyl / +42.011 Da (K)
5. Dynamic Modification:  Phospho / +79.966 Da (S, T, Y)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl / +57.021 Da (C)

------------------------------------------------------------------------------
Processing node 5: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05

------------------------------------------------------------------------------
Processing node 6: Mascot
------------------------------------------------------------------------------

1. Input Data:
-----------------------------
Protein Database:  CannabisProteins_95069seqs_Feb2020_noinvalidchar
Enzyme Name:  Trypsin
Maximum Missed Cleavage Sites:  9
Instrument:  ESI-TRAP
Taxonomy:  All entries

1.1 Peptide Scoring Options:
-----------------------------
Peptide Cut Off Score:  10
Peptide Without Protein Cut Off Score:  5

1.2 Protein Scoring Options:
-----------------------------
Use MudPIT Scoring:  Automatic
Protein Relevance Threshold:  20
Protein Relevance Factor:  1

2. Tolerances:
-----------------------------
Precursor Mass Tolerance:  10 ppm
Fragment Mass Tolerance:  0.8 Da
Use Average Precursor Mass:  False

4. Dynamic Modifications:
-----------------------------
1. Dynamic Modification:  Acetyl (N-term)
2. Dynamic Modification:  Oxidation (M)
3. Dynamic Modification:  Acetyl (K)
4. Dynamic Modification:  Methyl (K)
5. Dynamic Modification:  Phospho (ST)
6. Dynamic Modification:  Phospho (Y)
7. Dynamic Modification:  NAG (N)

5. Static Modifications:
-----------------------------
1. Static Modification:  Carbamidomethyl (C)

------------------------------------------------------------------------------
Processing node 7: Target Decoy PSM Validator
------------------------------------------------------------------------------

1. Decoy Database Search:
-----------------------------
Target FDR (Strict):  0.01
Target FDR (Relaxed):  0.05


================================================================================

Further information:

SEQUEST (4):
 - Number of sequences searched: 76645
Mascot (6):
 - Fasta database information: FASTA db: CannabisProteins_95069seqs_Feb2020_noinvalidchar_20200211.fasta
Version: 2.6
Number of sequences: 95069
Number of sequences after taxonomy: 95069
Taxonomy: 
Enzyme: 
Number of queries: 10671

 - MudPitScoring: True

================================================================================

Processing details:

03/22/2020 11:56 AM	(6):Mascot:	Total search time was 5 h 43 min.
03/22/2020 11:56 AM	(6):Mascot:	Search completed
03/22/2020 11:56 AM	(6):Mascot:	5108 protein(s) + 3027 decoy proteins scored and inserted into result file in 31.7 s.
03/22/2020 11:56 AM	(6):Mascot:	5108 protein(s) scored
03/22/2020 11:55 AM	(6):Mascot:	Search result finalization started.
03/22/2020 11:55 AM	(7):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/22/2020 11:55 AM	(7):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/22/2020 11:55 AM	(7):Target Decoy PSM Validator:	Evaluating peptides of Mascot (6) started
03/22/2020 11:55 AM	(6):Mascot:	Used mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/22/2020 11:55 AM	(6):Mascot:	Sending 10632 peptide hits (104711 peptides) to result file
03/22/2020 11:54 AM	(6):Mascot:	Sending 10622 decoy peptide hits (104420 peptides) to result file
03/22/2020 11:54 AM	(6):Mascot:	Reading decoy results
03/22/2020 11:54 AM	(6):Mascot:	Start translating results
03/22/2020 11:54 AM	(6):Mascot:	Start mapping modifications
03/22/2020 11:54 AM	(6):Mascot:	Received 7709 proteins from Mascot server
03/22/2020 11:54 AM	(6):Mascot:	Start mapping 7709 proteins
03/22/2020 11:53 AM	(6):Mascot:	Start parsing results
03/22/2020 11:53 AM	(6):Mascot:	Received Mascot result file (filename=../data/20200322/F019504.dat)
03/22/2020 11:53 AM	(6):Mascot:	Mascot Server completed
03/22/2020 06:11 AM	(6):Mascot:	Mascot result on server (filename=../data/20200322/F019504.dat)
03/22/2020 06:11 AM	(6):Mascot:	Start searching 10671 spectra
03/22/2020 06:11 AM	(4):SEQUEST:	Total search time was 2 h 19 min.
03/22/2020 06:11 AM	(4):SEQUEST:	Search completed
03/22/2020 06:11 AM	(4):SEQUEST:	37944 protein(s) + 36720 decoy proteins scored and inserted into result file in 1 min 16 s.
03/22/2020 06:11 AM	(4):SEQUEST:	37944 protein(s) scored
03/22/2020 06:09 AM	(4):SEQUEST:	Search result finalization started.
03/22/2020 06:09 AM	(5):Target Decoy PSM Validator:	Start calculating relaxed False Discovery Rate
03/22/2020 06:09 AM	(5):Target Decoy PSM Validator:	Start calculating strict False Discovery Rate
03/22/2020 06:08 AM	(5):Target Decoy PSM Validator:	Evaluating peptides of SEQUEST (4) started
03/22/2020 06:08 AM	(4):SEQUEST:	Sending 671 decoy peptide hits (6600 peptides) to result file
03/22/2020 06:01 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 06:01 AM	(4):SEQUEST:	Sending 671 peptide hits (6600 peptides) to result file
03/22/2020 05:54 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 10000 - 10671)
03/22/2020 05:54 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9940 peptides) to result file
03/22/2020 05:29 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 05:29 AM	(4):SEQUEST:	Sending 1000 peptide hits (9947 peptides) to result file
03/22/2020 05:05 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 9000 - 10000)
03/22/2020 05:04 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 04:50 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 04:50 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 04:36 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 8000 - 9000)
03/22/2020 04:36 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 04:28 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 04:28 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 04:21 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 7000 - 8000)
03/22/2020 04:21 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9990 peptides) to result file
03/22/2020 04:15 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 04:15 AM	(4):SEQUEST:	Sending 1000 peptide hits (9990 peptides) to result file
03/22/2020 04:10 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 6000 - 7000)
03/22/2020 04:10 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 04:06 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 04:06 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 04:03 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 5000 - 6000)
03/22/2020 04:03 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 04:01 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 04:01 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 03:59 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 4000 - 5000)
03/22/2020 03:58 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9994 peptides) to result file
03/22/2020 03:56 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 03:56 AM	(4):SEQUEST:	Sending 1000 peptide hits (9990 peptides) to result file
03/22/2020 03:54 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 3000 - 4000)
03/22/2020 03:54 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 03:53 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 03:53 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 03:51 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 2000 - 3000)
03/22/2020 03:51 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (9998 peptides) to result file
03/22/2020 03:50 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 03:50 AM	(4):SEQUEST:	Sending 1000 peptide hits (9994 peptides) to result file
03/22/2020 03:49 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 1000 - 2000)
03/22/2020 03:49 AM	(6):Mascot:	Use mascot server http://mascot.bioinf.science.depi.vic.gov.au/mascot/ with Mascot version 2.6.1
03/22/2020 03:49 AM	(4):SEQUEST:	Sending 1000 decoy peptide hits (10000 peptides) to result file
03/22/2020 03:48 AM	(4):SEQUEST:	Starting SEQUEST decoy search
03/22/2020 03:48 AM	(4):SEQUEST:	Sending 1000 peptide hits (10000 peptides) to result file
03/22/2020 03:46 AM	(4):SEQUEST:	Starting SEQUEST (search spectra 0 - 1000)
03/22/2020 03:46 AM	(4):SEQUEST:	There is already an adequate decoy FASTA index.
03/22/2020 03:46 AM	(4):SEQUEST:	Looking for existing decoy FASTA index.
03/22/2020 03:46 AM	(4):SEQUEST:	There is already an adequate target FASTA index.
03/22/2020 03:46 AM	(4):SEQUEST:	Looking for existing target FASTA index.
03/22/2020 03:46 AM	(1):Spectrum Selector:	Reading from File 1 of 1:bud3_T.raw (12330 spectra total)
