Example Proteome Discoverer evidence file from the output of a label free experiment
Source:R/dataDoc.R
pd_psm_input.RdExperiment was performed by the Olsen lab and published on Nat. Commun. (citation below).
Details
Bekker-Jensen, D.B., Bernhardt, O.M., Hogrebe, A. et al. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat Commun 11, 787 (2020). https://doi.org/10.1038/s41467-020-14609-1
The experiment was processed using Proteome Discoverer by the computational proteomics team at Pfizer (Liang Xue and Pierre Jean).
The experiment did not contain a global profiling run, but we show an example of extracting the unmodified peptides and using them in place of the profiling run.
Examples
head(pd_psm_input)
#> Checked Tags Confidence Identifying.Node.Type Identifying.Node Search.ID
#> 1 False NA High Sequest HT Sequest HT (B4) B
#> 2 False NA High Sequest HT Sequest HT (B4) B
#> 3 False NA High Sequest HT Sequest HT (B4) B
#> 4 False NA High Sequest HT Sequest HT (B4) B
#> 5 False NA High Sequest HT Sequest HT (B4) B
#> 6 False NA High Sequest HT Sequest HT (B4) B
#> Identifying.Node.No PSM.Ambiguity Sequence
#> 1 4 Unambiguous AAEAGETGAATSATEGDNNNNTAAGDKK
#> 2 4 Unambiguous LEAGLSDSK
#> 3 4 Unambiguous LQETNPEEVPK
#> 4 4 Unambiguous LREENFSSNTSELGNKK
#> 5 4 Unambiguous LLDNTNTDVK
#> 6 4 Selected HSDSYSENETNHTNVPISSTGGTNNK
#> Annotated.Sequence Modifications X..Proteins
#> 1 [K].AAEAGETGAATSATEGDNNNNTAAGDKK.[G] 1
#> 2 [K].LEAGLsDSK.[Q] S6(Phospho) 1
#> 3 [K].LQETNPEEVPK.[F] 1
#> 4 [K].LREENFSSNtSELGNKK.[H] T10(Phospho) 1
#> 5 [K].LLDNTNTDVK.[I] 1
#> 6 [R].HSDSYsENETNHTNVPISSTGGTNNK.[T] S6(Phospho) 20
#> Master.Protein.Accessions
#> 1 Q07478
#> 2 P17536
#> 3 P35691
#> 4 P33419
#> 5 Q08421
#> 6 Q99231
#> Master.Protein.Descriptions
#> 1 ATP-dependent RNA helicase SUB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SUB2 PE=1 SV=1
#> 2 Tropomyosin-1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TPM1 PE=1 SV=1
#> 3 Translationally-controlled tumor protein homolog OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TMA19 PE=1 SV=1
#> 4 Spindle pole component 29 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SPC29 PE=1 SV=1
#> 5 Enhancer of translation termination 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=ETT1 PE=1 SV=1
#> 6 Transposon Ty1-DR3 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR3 PE=1 SV=2
#> Protein.Accessions
#> 1 Q07478
#> 2 P17536
#> 3 P35691
#> 4 P33419
#> 5 Q08421
#> 6 P0C2I9; P47100; Q12141; P47098; P0C2J0; P0C2I3; Q12269; Q03855; P0C2I2; Q99231; Q12414; Q07793; Q04711; Q04670; Q12273; Q03612; Q92393; P0C2I5; Q03434; O13527
#> Protein.Descriptions
#> 1 ATP-dependent RNA helicase SUB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SUB2 PE=1 SV=1
#> 2 Tropomyosin-1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TPM1 PE=1 SV=1
#> 3 Translationally-controlled tumor protein homolog OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TMA19 PE=1 SV=1
#> 4 Spindle pole component 29 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=SPC29 PE=1 SV=1
#> 5 Enhancer of translation termination 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=ETT1 PE=1 SV=1
#> 6 Transposon Ty1-PR1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-PR1 PE=3 SV=1; Transposon Ty1-JR2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-JR2 PE=3 SV=3; Transposon Ty1-GR1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-GR1 PE=3 SV=1; Transposon Ty1-JR1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-JR1 PE=3 SV=3; Transposon Ty1-PR2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-PR2 PE=3 SV=1; Transposon Ty1-DR6 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR6 PE=3 SV=1; Transposon Ty1-GR2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-GR2 PE=3 SV=3; Transposon Ty1-DR1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR1 PE=3 SV=2; Transposon Ty1-DR5 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR5 PE=3 SV=1; Transposon Ty1-DR3 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR3 PE=1 SV=2; Transposon Ty1-PL Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-PL PE=3 SV=1; Transposon Ty1-DR4 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-DR4 PE=3 SV=2; Transposon Ty1-ML1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-ML1 PE=3 SV=2; Transposon Ty1-MR2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-MR2 PE=3 SV=2; Transposon Ty1-OL Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-OL PE=3 SV=1; Transposon Ty1-ER1 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-ER1 PE=3 SV=1; Transposon Ty1-OR Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-OR PE=3 SV=1; Transposon Ty1-LR2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-LR2 PE=3 SV=1; Transposon Ty1-ML2 Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-ML2 PE=3 SV=2; Truncated transposon Ty1-A Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY1B-A PE=3 SV=3
#> X..Missed.Cleavages Charge Original.Precursor.Charge DeltaScore DeltaCn Rank
#> 1 1 3 3 0.7340 0 1
#> 2 0 2 2 0.1038 0 1
#> 3 0 2 2 0.4962 0 1
#> 4 2 3 3 0.1122 0 1
#> 5 0 2 2 0.5480 0 1
#> 6 0 3 3 0.0091 0 1
#> Search.Engine.Rank Concatenated.Rank m.z..Da. Contaminant Aligned.m.z..Da.
#> 1 1 1 879.3940 False 879.3940
#> 2 1 1 500.2237 False 500.2237
#> 3 1 1 642.3285 False 642.3285
#> 4 1 1 678.3174 False 678.3174
#> 5 1 1 566.7962 False 566.7962
#> 6 1 1 957.4013 False 957.4013
#> MH...Da. Theo..MH...Da. DeltaM..ppm. Deltam.z..Da. Ions.Matched Matched.Ions
#> 1 2636.1673 2636.1667 0.25 0.00022 0/0 0
#> 2 999.4401 999.4394 0.64 0.00032 0/0 0
#> 3 1283.6497 1283.6478 1.47 0.00094 0/0 0
#> 4 2032.9376 2032.9335 2.00 0.00135 0/0 0
#> 5 1132.5851 1132.5844 0.57 0.00032 0/0 0
#> 6 2870.1893 2870.1861 1.14 0.00109 0/0 0
#> Total.Ions Intensity Activation.Type NCE.... MS.Order
#> 1 0 7769382 HCD 28 MS2
#> 2 0 2978492 HCD 28 MS2
#> 3 0 2776155 HCD 28 MS2
#> 4 0 2369740 HCD 28 MS2
#> 5 0 2483459 HCD 28 MS2
#> 6 0 4993433 HCD 28 MS2
#> Isolation.Interference.... Ion.Inject.Time..ms. RT..min. First.Scan Last.Scan
#> 1 1.321094 22 4.9337 1851 1851
#> 2 25.545490 22 7.5681 5317 5317
#> 3 10.363530 22 7.5687 5318 5318
#> 4 6.098627 22 7.5720 5320 5320
#> 5 24.051600 22 7.5726 5321 5321
#> 6 0.000000 22 7.5738 5323 5323
#> Master.Scan.s. Spectrum.File File.ID Quan.Info
#> 1 1848 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> 2 5306 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> 3 5306 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> 4 5319 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> 5 5319 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> 6 5319 20180810_QE3_nLC3_AH_DDA_Yonly_ind_02.raw F35
#> Peptides.Matched XCorr X..Protein.Groups Percolator.q.Value Percolator.PEP
#> 1 3606 8.57 1 0.0001142857 6.305117e-16
#> 2 679 2.60 1 0.0001143000 3.711000e-04
#> 3 511 2.62 1 0.0001143000 1.498000e-05
#> 4 1894 5.26 1 0.0001143000 3.015000e-07
#> 5 505 2.50 1 0.0001143000 7.418000e-05
#> 6 2549 7.66 1 0.0001143000 6.116000e-14
#> Percolator.SVMScore Precursor.Area Apex.RT..min.
#> 1 9.869511 5859362 4.94
#> 2 1.135000 5397380 7.58
#> 3 1.719000 66213752 7.61
#> 4 2.428000 NA NA
#> 5 1.428000 1715639 7.56
#> 6 5.227000 22296560 7.59
#> ptmRS..Binomial.Peptide.Score ptmRS..Isoform.Confidence.Probability
#> 1 NA NA
#> 2 308.92 1.000
#> 3 NA NA
#> 4 439.90 1.000
#> 5 NA NA
#> 6 611.48 0.006
#> ptmRS..Isoform.Group.Report
#> 1
#> 2 y1+-H(3) O(4) P(8): 788.38; y1+-H(3) O(4) P(7): 659.34; y1+-H(3) O(4) P(6): 588.30; y1+-H(3) O(4) P(5): 531.28; y1+-H(3) O(4) P(4): 418.19; y2+-H(3) O(4) P(6): 294.65; y1+(3): 349.17; y1+(2): 234.14
#> 3
#> 4 b1+-H(3) O(4) P(10): 1160.53; b1+-H(3) O(4) P(12): 1376.61; y1+-H(3) O(4) P(10): 1059.54; y1+-H(3) O(4) P(9): 972.51; y1+-H(3) O(4) P(8): 858.47; y2+-H(3) O(4) P(10): 530.28; y2+-H(3) O(4) P(9): 486.76; y2+-H(3) O(4) P(8): 429.74; y1+(7): 775.43; y2+(7): 388.22
#> 5
#> 6 b1+-H(3) O(4) P(4): 409.15; b1+-H(3) O(4) P(5): 572.21; b1+-H(3) O(4) P(6): 659.24; b1+-H(3) O(4) P(9): 1031.37; b1+-H(3) O(4) P(10): 1132.42; b1+-H(3) O(4) P(11): 1246.46; b1+-H(3) O(4) P(12): 1383.52; b1+-H(3) O(4) P(14): 1598.61; b1+-H(3) O(4) P(15): 1697.68; b2+-H(3) O(4) P(9): 516.19; b2+-H(3) O(4) P(12): 692.26; b2+-H(3) O(4) P(13): 742.79; b2+-H(3) O(4) P(14): 799.81; b2+-H(3) O(4) P(15): 849.34; y2+-H(3) O(4) P(25): 1318.08; y2+-H(3) O(4) P(24): 1274.56; y2+-H(3) O(4) P(23): 1217.05
#> ptmRS..Best.Site.Probabilities
#> 1
#> 2 S6(Phospho): 100
#> 3
#> 4 T10(Phospho): 100
#> 5
#> 6 S4(Phospho): 99.4
#> ptmRS..Phospho.Site.Probabilities
#> 1
#> 2 S(6): 100.0; S(8): 0.0
#> 3
#> 4 S(7): 0.0; S(8): 0.0; T(10): 100.0; S(11): 0.0
#> 5
#> 6 S(2): 0.0; S(4): 99.4; Y(5): 0.0; S(6): 0.6; T(10): 0.0; T(13): 0.0; S(18): 0.0; S(19): 0.0; T(20): 0.0; T(23): 0.0