It can be the output of MSstatsPTM converter MaxQtoMSstatsPTMFormat or other MSstatsTMT converter functions (Please see MSstatsPTM_TMT_Workflow vignette). The dataset is formatted as a list with two data.tables named PTM and PROTEIN. In each data.table the variables are as follows:
raw.input.tmt
A list of two data.tables named PTM and PROTEIN with 1716 and 29221 rows respectively.
ProteinName : Name of protein with modification site mapped in with an underscore. ie "Protein_4_Y474"
PeptideSequence
Charge
PSM
Mixture : Mixture of samples labeled with different TMT reagents,
which can be analyzed in
a single mass spectrometry experiment. If the channal doesn't have sample,
please add Empty' under Condition. \item TechRepMixture : Technical replicate of one mixture. One mixture may have multiple technical replicates. For example, if TechRepMixture' = 1, 2 are the two technical replicates of
one mixture, then they should match
with same Mixture' value. \item Run : MS run ID. \item Channel : Labeling information (126, ... 131). \item Condition : Condition (ex. Healthy, Cancer, Time0) \item BioReplicate : Unique ID for biological subject. If the channal doesn't have sample, please add Empty' under BioReplicate.
Intensity
#> ProteinName PeptideSequence Charge PSM Mixture TechRepMixture #> 1 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> 2 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> 3 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> 4 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> 5 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> 6 Protein_12_S703 Peptide491 3 Peptide_491_3 1 1 #> Run Channel Condition BioReplicate Intensity #> 1 1_1 128N Condition_2 Condition_2_1 48030.0 #> 2 1_1 129C Condition_4 Condition_4_2 100224.4 #> 3 1_1 131C Condition_3 Condition_3_2 66804.6 #> 4 1_1 130N Condition_1 Condition_1_2 46779.8 #> 5 1_1 128C Condition_6 Condition_6_1 77497.9 #> 6 1_1 126C Condition_4 Condition_4_1 81559.7#> ProteinName PeptideSequence Charge PSM Mixture TechRepMixture Run #> 1 Protein_12 Peptide9121 3 Peptide_9121_3 1 1 1_1 #> 2 Protein_12 Peptide27963 5 Peptide_27963_5 1 1 1_1 #> 3 Protein_12 Peptide28482 4 Peptide_28482_4 1 1 1_1 #> 4 Protein_12 Peptide10940 2 Peptide_10940_2 2 1 2_1 #> 5 Protein_12 Peptide4900 2 Peptide_4900_2 2 1 2_1 #> 6 Protein_12 Peptide4900 3 Peptide_4900_3 2 1 2_1 #> Channel Condition BioReplicate Intensity #> 1 126C Condition_4 Condition_4_1 10996116.9 #> 2 127C Condition_5 Condition_5_1 56965.1 #> 3 131N Condition_2 Condition_2_2 286121.7 #> 4 131N Condition_2 Condition_2_4 534806.0 #> 5 126C Condition_4 Condition_4_3 1134908.7 #> 6 126C Condition_4 Condition_4_3 1605773.2