Example of output from PDtoMSstatsTMTFormat function

It is made from raw.pd and annotation.pd, which is the output of PDtoMSstatsTMTFormat function. It should include the required columns as below. The variables are as follows:

input.pd

Format

A data frame with 20110 rows and 11 variables.

Details

  • ProteinName : Protein ID

  • PeptideSequence : peptide sequence

  • Charge : peptide charge

  • PSM : peptide ion and spectra match

  • Channel : Labeling information (126, ... 131)

  • Condition : Condition (ex. Healthy, Cancer, Time0)

  • BioReplicate : Unique ID for biological subject.

  • Run : MS run ID

  • Mixture : Unique ID for TMT mixture.

  • TechRepMixture : Unique ID for technical replicate of one TMT mixture.

  • Intensity: Protein Abundance

Examples

head(input.pd)

#>   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