MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.

Notes

• MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required, which has to be in the format 'channel.X' with X being the channel number..

  #>            ProteinName                               PeptideSequence
  #> 1 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #> 2 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #> 3 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #> 4 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #> 5 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #> 6 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
  #>   Charge                                             PSM Mixture
  #> 1               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #> 2               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #> 3               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #> 4               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #> 5               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #> 6               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
  #>   TechRepMixture   Run         Channel BioReplicate Condition Intensity
  #> 1            3_3 3_3_3       channel.1           21   Long_HF        NA
  #> 2            3_3 3_3_3       channel.2           22      Norm  1068.580
  #> 3            3_3 3_3_3       channel.3           23    Long_M  1508.330
  #> 4            3_3 3_3_3       channel.4           24   Long_HF        NA
  #> 5            3_3 3_3_3       channel.5           25   Long_LF  1580.951
  #> 6            3_3 3_3_3       channel.6           26   Long_HF  1820.072
  

  For more information please visit the MSstatsConvert documentation

• Comparison matrix as tabular file

  • 1st column: name of comparison

  • additionally one column for each condition that is present in the tabular file. Use 1 and -1 to indicate the conditions to compare and 0 for conditions that are not compared. Multiple groups can be combined by using 0.5.

  • first row contains the names of the groups, they must exactly match the condition name used in the annotation file

  • each additional row represents one comparison

  • Example for a two group comparison

         names     groupA  groupB
    groupA-groupB    1      -1
    

  • Example for an experiment with 5 groups and 4 different comparisons

      names    G1   G2   G3   G4   G5
      G2-G1    -1    1    0    0    0
      G4-G5     0    0    0    1   -1
      G3-G5     0    0   -1    0    1
    G1+G2-G5    0.5  0.5  0    0   -1
    

For additional help please visit the MSstatsTMT documentation