PDtoMSstatsTMTFormat: Generate MSstatsTMT required input format from Proteome...

Description Usage Arguments Value Examples

View source: R/PDtoMSstatsTMTFormat.R

Description

Convert Proteome discoverer output into the required input format for MSstatsTMT.

Usage

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PDtoMSstatsTMTFormat(
  input,
  annotation,
  which.proteinid = "Protein.Accessions",
  useNumProteinsColumn = TRUE,
  useUniquePeptide = TRUE,
  rmPSM_withMissing_withinRun = FALSE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum
)

Arguments

input

data name of Proteome discover PSM output.

annotation

data frame which contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.pd' for the meaning of each column.

which.proteinid

Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein name with single protein.

useNumProteinsColumn

TURE(default) remove shared peptides by information of # Proteins column in PSM sheet.

useUniquePeptide

TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.

rmPSM_withMissing_withinRun

TRUE will remove PSM with any missing value within each Run. Defaut is FALSE.

rmPSM_withfewMea_withinRun

only for rmPSM_withMissing_withinRun = FALSE. TRUE(default) will remove the features that have 1 or 2 measurements within each Run.

rmProtein_with1Feature

TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.

summaryforMultipleRows

sum(default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.

Value

input for proteinSummarization function

Examples

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Example output

   Checked Confidence Identifying.Node PSM.Ambiguity
1:   FALSE       High      Mascot (O4)   Unambiguous
2:   FALSE       High      Mascot (K2)   Unambiguous
3:   FALSE       High      Mascot (K2)   Unambiguous
4:   FALSE       High      Mascot (F2)      Selected
5:   FALSE       High      Mascot (K2)   Unambiguous
6:   FALSE       High      Mascot (K2)   Unambiguous
                       Annotated.Sequence
1: [K].gFQQILAGEYDHLPEQAFYMVGPIEEAVAk.[A]
2:          [R].qYPWGVAEVENGEHcDFTILr.[N]
3:              [R].dkPSVEPVEEYDYEDLk.[E]
4:                      [R].hEHQVMLmr.[Q]
5:       [R].dNLTLWTADNAGEEGGEAPQEPQS.[-]
6:         [R].aLVAIGTHDLDTLSGPFTYTAk.[R]
                                                     Modifications Marked.as
1:                                 N-Term(TMT6plex); K30(TMT6plex)        NA
2: N-Term(TMT6plex); C15(Carbamidomethyl); R21(Label:13C(6)15N(4))        NA
3:                         N-Term(TMT6plex); K2(Label); K17(Label)        NA
4:         N-Term(TMT6plex); M8(Oxidation); R9(Label:13C(6)15N(4))        NA
5:                                                N-Term(TMT6plex)        NA
6:                                    N-Term(TMT6plex); K22(Label)        NA
   X..Protein.Groups X..Proteins Master.Protein.Accessions
1:                 1           1                    P06576
2:                 1           1                    Q16181
3:                 1           1                    Q9Y450
4:                 1           1                    Q15233
5:                 1           1                    P31947
6:                 1           1                    Q9NSD9
                                                           Master.Protein.Descriptions
1:         ATP synthase subunit beta, mitochondrial OS=Homo sapiens GN=ATP5B PE=1 SV=3
2:                                         Septin-7 OS=Homo sapiens GN=SEPT7 PE=1 SV=2
3:                                HBS1-like protein OS=Homo sapiens GN=HBS1L PE=1 SV=1
4: Non-POU domain-containing octamer-binding protein OS=Homo sapiens GN=NONO PE=1 SV=4
5:                               14-3-3 protein sigma OS=Homo sapiens GN=SFN PE=1 SV=1
6:          Phenylalanine--tRNA ligase beta subunit OS=Homo sapiens GN=FARSB PE=1 SV=3
   Protein.Accessions
1:             P06576
2:             Q16181
3:             Q9Y450
4:             Q15233
5:             P31947
6:             Q9NSD9
                                                                  Protein.Descriptions
1:         ATP synthase subunit beta, mitochondrial OS=Homo sapiens GN=ATP5B PE=1 SV=3
2:                                         Septin-7 OS=Homo sapiens GN=SEPT7 PE=1 SV=2
3:                                HBS1-like protein OS=Homo sapiens GN=HBS1L PE=1 SV=1
4: Non-POU domain-containing octamer-binding protein OS=Homo sapiens GN=NONO PE=1 SV=4
5:                               14-3-3 protein sigma OS=Homo sapiens GN=SFN PE=1 SV=1
6:          Phenylalanine--tRNA ligase beta subunit OS=Homo sapiens GN=FARSB PE=1 SV=3
   X..Missed.Cleavages Charge DeltaScore DeltaCn Rank Search.Engine.Rank
1:                   0      3     1.0000       0    1                  1
2:                   0      3     1.0000       0    1                  1
3:                   1      3     0.9730       0    1                  1
4:                   0      4     0.5250       0    1                  1
5:                   0      3     1.0000       0    1                  1
6:                   0      3     0.9783       0    1                  1
    m.z..Da. MH...Da. Theo..MH...Da. DeltaM..ppm. Deltam.z..Da. Activation.Type
1: 1270.3249 3808.960       3808.966        -1.51      -0.00192             CID
2:  920.4493 2759.333       2759.332         0.31       0.00028             CID
3:  920.1605 2758.467       2758.461         2.08       0.00192             CID
4:  359.6898 1435.737       1435.738        -0.04      -0.00002             CID
5:  920.0943 2758.268       2758.264         1.53       0.00141             CID
6:  919.8502 2757.536       2757.532         1.48       0.00136             CID
   MS.Order Isolation.Interference.... Average.Reporter.S.N
1:      MS2                  47.955590                  8.7
2:      MS2                   9.377507                  8.1
3:      MS2                  38.317050                 17.8
4:      MS2                  21.390040                 36.5
5:      MS2                   0.000000                 16.7
6:      MS2                  30.619960                 26.7
   Ion.Inject.Time..ms. RT..min. First.Scan
1:               50.000 212.2487     112815
2:                3.242 164.7507      87392
3:               13.596 143.4534      74786
4:               50.000  21.6426       6458
5:                6.723 174.1863      92950
6:                8.958 176.4863      94294
                                  Spectrum.File File.ID Abundance..126
1: 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03.raw      F1       2548.326
2: 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw      F5      22861.765
3: 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw      F5      25504.083
4: 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02.raw     F10      13493.228
5: 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw      F5      64582.786
6: 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03.raw      F5      35404.709
   Abundance..127N Abundance..127C Abundance..128N Abundance..128C
1:        3231.929        2760.839        4111.639        3127.254
2:       25817.946       23349.498       29449.609       25995.929
3:       27740.450       25144.974       25754.579       29923.176
4:       14674.490       11187.900       12831.495       13839.426
5:       50576.417       47126.037       56285.129       46257.310
6:       31905.852       30993.941       36854.351       37506.001
   Abundance..129N Abundance..129C Abundance..130N Abundance..130C
1:        1874.163        2831.423        2298.401        3798.876
2:       22955.769       30578.971       30660.488       38728.853
3:       34097.637       31650.255       27632.692       23886.881
4:       12441.353       13450.885       14777.844       13039.995
5:       52634.885       49716.850       60660.574       55830.488
6:       25703.444       38626.598       35447.942       33788.409
   Abundance..131 Quan.Info Ions.Score Identity.Strict Identity.Relaxed
1:       3739.067        NA         90              28               21
2:      25047.280        NA         76              24               17
3:      35331.092        NA         74              30               23
4:      12057.121        NA         40              25               18
5:      40280.577        NA         38              21               14
6:      32031.516        NA         46              29               22
   Expectation.Value Percolator.q.Value Percolator.PEP
1:      7.038672e-09                  0      1.396e-05
2:      6.298627e-08                  0      3.349e-07
3:      4.318385e-07                  0      9.922e-07
4:      3.351211e-04                  0      1.175e-04
5:      2.152501e-04                  0      1.383e-05
6:      2.060469e-04                  0      7.198e-05
                                           Run Fraction TechRepMixture Channel
1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1     126
2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    127N
3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    127C
4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    128N
5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    128C
6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw        1              1    129N
  Condition  Mixture   BioReplicate
1      Norm Mixture1  Mixture1_Norm
2     0.667 Mixture1 Mixture1_0.667
3     0.125 Mixture1 Mixture1_0.125
4       0.5 Mixture1   Mixture1_0.5
5         1 Mixture1     Mixture1_1
6     0.125 Mixture1 Mixture1_0.125
** Shared PSMs (assigned in multiple proteins) are removed.
** 55 features have 1 or 2 intensities across runs and are removed.
** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows.
  ProteinName               PeptideSequence Charge
1      P04406        [K].lISWYDNEFGYSNR.[V]      2
2      Q9NSD9           [K].irPFAVAAVLr.[N]      3
3      P04406    [K].lVINGNPITIFQErDPSk.[I]      3
4      P04406          [R].vVDLmAHMASkE.[-]      3
5      P06576      [R].dQEGQDVLLFIDNIFR.[F]      3
6      P06576 [R].iPSAVGYQPTLATDMGTMQEr.[I]      3
                              PSM  Mixture TechRepMixture
1        [K].lISWYDNEFGYSNR.[V]_2 Mixture1              1
2           [K].irPFAVAAVLr.[N]_3 Mixture1              1
3    [K].lVINGNPITIFQErDPSk.[I]_3 Mixture1              1
4          [R].vVDLmAHMASkE.[-]_3 Mixture1              1
5      [R].dQEGQDVLLFIDNIFR.[F]_3 Mixture1              1
6 [R].iPSAVGYQPTLATDMGTMQEr.[I]_3 Mixture1              1
                                           Run Channel Condition  BioReplicate
1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01.raw     126      Norm Mixture1_Norm
    Intensity
1    8348.351
2   28327.492
3 1275010.965
4   80589.877
5    2231.389
6  144854.307

MSstatsTMT documentation built on Dec. 20, 2020, 2:01 a.m.