It can be the output of PDtoMSstatsTMTFormat or other MSstatsTMT converter functions. It includes peak intensities for a variety of PTMs. This is the companion file to the raw.ptm dataset, includes unmodified protein data. The variables are as follows:
A data frame with 620476 rows and 11 variables.
ProteinName : Name of protein
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,
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
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.
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