Annotated spectra of M_02_23_E2_ETD.msf

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Peptides

Confidence Sequence Activation Type Modifications IonScore ΔScore Rank Search Engine Charge Precursor m/z [Da] ΔM [ppm] First Scan Last Scan Annotated Spectrum Peak List
High RLSRPGsGSVSGLASQR ETD S7(PhospR4) 29.38 1.00 1 Mascot (3) 3 598.97101 0.75 613 613 Image Peak List
High IIGVDFNsKRFDQAK ETD S8(PhospR4) 39.41 1.00 1 Mascot (3) 3 606.63727 1.42 1454 1454 Image Peak List
High KEEKEEsDDDMGFSLFE ETD S7(PhospR4) 72.24 1.00 1 Mascot (3) 3 705.61285 4.31 2176 2176 Image Peak List
High RKPISDEVNDsDEEYKK ETD S11(PhospR4) 27.23 1.00 1 Mascot (3) 3 711.32397 1.38 210 210 Image Peak List
High VAVPDTQPLSNPPRtPMKK ETD T15(PhospR4) 44.13 0.36 1 Mascot (3) 3 719.37061 1.76 968 968 Image Peak List
High tPPTNASLDYPSADSEHVSK ETD T1(PhospR4) 25.89 1.00 1 Mascot (3) 3 732.65472 0.14 1080 1080 Image Peak List
High LHTVPEVAEEEGDKDEYHDAsDKQ ETD S21(PhospR4) 31.42 1.00 1 Mascot (3) 3 941.06641 0.33 753 753 Image Peak List
High VHDDDEDVSsEDENETHNSNAVYYK ETD S10(PhospR4) 25.35 1.00 1 Mascot (3) 3 997.72253 3.13 765 765 Image Peak List
High EFVLINEDESEYDtEMsGDDEVAKPLVSK ETD T14(PhospR4); S17(PhospR4) 45.10 0.36 1 Mascot (3) 3 1150.14648 -1.95 2486 2486 Image Peak List
High GNSVPATAPTPIPLVSINHDDDDDEsDDDFLQLAHR ETD S26(PhospR4) 26.39 1.00 1 Mascot (3) 3 1322.92590 -0.90 2479 2479 Image Peak List
High KDNADMTSDLTGTIESADSAIPNSPtEDAAPGNIQDLK ETD T26(PhospR4) 29.30 0.07 1 Mascot (3) 3 1328.26526 1.58 2218 2218 Image Peak List

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Search Summary

Workflow created with Discoverer version: 1.2.0.208 (DBVersion:53)

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Search name: M15_CS23_incl_022012_Excl2_ETD
Search description: -
Search date: 03/25/2013 10:13:43

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The pipeline tree:
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    |-(0) Spectrum Files
        |-(1) Spectrum Selector
            |-(2) Non-Fragment Filter
                |-(3) Mascot

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

Search name: M15_CS23_incl_022012_Excl2_ETD
Search description: -
Search date: 03/25/2013 10:13:43

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

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

    |-(0) Spectrum Files
        |-(1) Spectrum Selector
            |-(2) Non-Fragment Filter
                |-(3) Mascot

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Processing node 0: Spectrum Files
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Input Data:
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File Name(s): F:\Raw files\022012\M15_CS23_incl_022012_Excl2.raw

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Processing node 1: Spectrum Selector
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1. General Settings:
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Precursor Selection: Use MS1 Precursor
Use New Precursor Reevaluation: True

2. Spectrum Properties Filter:
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Lower RT Limit: 0
Upper RT Limit: 0
Lowest Charge State: 0
Highest Charge State: 0
Min. Precursor Mass: 400 Da
Max. Precursor Mass: 10000 Da
Total Intensity Threshold: 0
Minimum Peak Count: 1

3. Scan Event Filters:
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MS Order: Is MS2
Activation Type: Is ETD
Scan Type: Is Full

4. Peak Filters:
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S/N Threshold (FT-only): 3

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

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Processing node 2: Non-Fragment Filter
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1. Precursor Peaks:
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Remove Precursor Peak: True
Mass Window Offset: 4 Da

2. Charge Reduced Precursors:
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Remove Charge Reduced Precursors: True
Mass Window Offset: 2 Da

3. Neutral Losses From Charge Reduced Precursors:
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Remove Neutral Loss Peaks: True
Mass Window Offset: 2 Da
Remove Only Known Masses: True
Maximum Neutral Loss Mass: 120 Da

4. FT Overtones:
-----------------------------
Remove Precursor Overtones: False
Mass Window Offset: 0.5 Da

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Processing node 3: Mascot
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1. Input Data:
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Protein Database: TAIR10
Enzyme Name: Trypsin
Maximum Missed Cleavage Sites: 2
Instrument: ETD-TRAP
Taxonomy: All entries

1.1 Peptide Scoring Options:
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Peptide Cut Off Score: 10

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

2. Decoy Database Search:
-----------------------------
Decoy Search: True

3. Tolerances:
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Precursor Mass Tolerance: 5 ppm
Fragment Mass Tolerance: 0.6 Da
Use Average Precursor Mass: False

4. Decoy Database Search:
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Significance High: 0.0656
Significance Middle: 0.09

4. Dynamic Modifications:
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1. Dynamic Modification: Phosphogood (ST)
2. Dynamic Modification: Phospho (Y)

5. Static Modifications:
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1. Static Modification: Methylthio (C)

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Processing details:

03/25/2013 10:18 AM (3):Mascot: Search completed
03/25/2013 10:18 AM (3):Mascot: 33 protein(s) scored and inserted into result file in 1.95 s
03/25/2013 10:18 AM (3):Mascot: ScoreCalculator: 33 protein(s) scored
03/25/2013 10:18 AM (3):Mascot: Result finalization started
03/25/2013 10:18 AM (3):Mascot: Start calculating relaxed FDR
03/25/2013 10:18 AM (3):Mascot: Start calculating strict FDR
03/25/2013 10:18 AM (3):Mascot: Used mascot server http://mascot/mascot/ with Mascot version 2.2.7
03/25/2013 10:18 AM (3):Mascot: Sending 98 peptide hits (239 peptides) to result file
03/25/2013 10:18 AM (3):Mascot: Sending 50 decoy peptide hits (178 peptides) to result file
03/25/2013 10:18 AM (3):Mascot: Reading decoy results
03/25/2013 10:18 AM (3):Mascot: Start translating results
03/25/2013 10:18 AM (3):Mascot: Start mapping modifications
03/25/2013 10:18 AM (3):Mascot: Received 46 proteins from Mascot server
03/25/2013 10:18 AM (3):Mascot: Start mapping 46 proteins
03/25/2013 10:18 AM (3):Mascot: Start parsing results
03/25/2013 10:18 AM (3):Mascot: Received Mascot result file (filename=../data/20130325/F007455.dat)
03/25/2013 10:18 AM (3):Mascot: Mascot Server completed
03/25/2013 10:17 AM (3):Mascot: Mascot result on server (filename=../data/20130325/F007455.dat)
03/25/2013 10:17 AM (3):Mascot: Start searching 3200 spectra
03/25/2013 10:17 AM (2):Non-Fragment Filter: Sending 200 spectra to Mascot
03/25/2013 10:17 AM (2):Non-Fragment Filter: Sending 200 spectra to result file
03/25/2013 10:17 AM (2):Non-Fragment Filter: Receiving spectra 3001 to 3201.
03/25/2013 10:17 AM (1):Spectrum Selector: Sending 200 spectra to Spectrum Distributor
03/25/2013 10:17 AM (2):Non-Fragment Filter: Sending 1000 spectra to Mascot
03/25/2013 10:17 AM (2):Non-Fragment Filter: Sending 1000 spectra to result file
03/25/2013 10:17 AM (2):Non-Fragment Filter: Receiving spectra 2001 to 3001.
03/25/2013 10:17 AM (1):Spectrum Selector: Sending 1000 spectra to Spectrum Distributor
03/25/2013 10:17 AM (2):Non-Fragment Filter: Sending 1000 spectra to Mascot
03/25/2013 10:16 AM (2):Non-Fragment Filter: Sending 1000 spectra to result file
03/25/2013 10:16 AM (2):Non-Fragment Filter: Receiving spectra 1001 to 2001.
03/25/2013 10:16 AM (1):Spectrum Selector: Sending 1000 spectra to Spectrum Distributor
03/25/2013 10:16 AM (3):Mascot: Use mascot server http://mascot/mascot/ with Mascot version 2.2.7
03/25/2013 10:16 AM (2):Non-Fragment Filter: Sending 1000 spectra to Mascot
03/25/2013 10:16 AM (2):Non-Fragment Filter: Sending 1000 spectra to result file
03/25/2013 10:16 AM (2):Non-Fragment Filter: Receiving spectra 1 to 1001.
03/25/2013 10:16 AM (1):Spectrum Selector: Sending 1000 spectra to Spectrum Distributor


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