Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.

Example of MSstatsTMT PSM sheet from MaxQuant. It is the input for OpenMStoMSstatsTMTFormat function. It includes peak intensities for 10 proteins among 27 MS runs from three TMT10 mixtures. The important variables are as follows:

raw.om

Format

A data frame with 860 rows and 13 variables.

Details

  • RetentionTime

  • ProteinName

  • PeptideSequence

  • Charge

  • Channel

  • Condition

  • BioReplicate

  • Run

  • Mixture

  • TechRepMixture

  • Fraction

  • Intensity

  • Reference

Examples

head(raw.om)

#>   RetentionTime          ProteinName                 PeptideSequence Charge
#> 1      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#> 2      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#> 3      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#> 4      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#> 5      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#> 6      2924.491 sp|P11679|K2C8_MOUSE .(TMT6plex)AEAETMYQIK(TMT6plex)      2
#>   Channel Condition BioReplicate   Run Mixture TechRepMixture Fraction
#> 1       1   Long_LF            1 1_1_3       1            1_1        3
#> 2       2   Long_LF            2 1_1_3       1            1_1        3
#> 3       3    Long_M            3 1_1_3       1            1_1        3
#> 4       6    Long_M            6 1_1_3       1            1_1        3
#> 5       5      Norm            5 1_1_3       1            1_1        3
#> 6       9      Norm            9 1_1_3       1            1_1        3
#>   Intensity
#> 1  5727.319
#> 2  6985.365
#> 3  4553.897
#> 4  5937.782
#> 5  5151.292
#> 6  6800.128
#>                                                                                                          Reference
#> 1 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324
#> 2 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324
#> 3 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324
#> 4 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324
#> 5 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324
#> 6 PAMI-176_Mouse_A-J_TMT_40ug_22pctACN_25cm_120min_20160223_OT.mzML_controllerType=0 controllerNumber=1 scan=11324