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The pmartRqc package provides functionality for quality control (QC) processing of mass spectrometry (MS) pan-omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, and data summarization (correlation, principal components analysis).

Figure 1. Workflow capabilities available in pmartRqc.

Sample datasets are available in the pmartRdata package for each of the following data types: peptide level data, protein level data, lipidomic data, and metabolomic data. Under development are 3 additional packages that will contain functionality for processing MS omics data. These are pmartRstat for statistical analysis, pmartRpq for protein quantification of peptide level data, and pmartRviz for visualization of the data incorporating the statistical results.

A vignette is available inside the pmartRqc package that demonstrates how to use the functions in the package for the quality control of proteomic data at the peptide level.