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PRMkit is a software package for processing parallel reaction monitoring (PRM) data in the context of targeted proteomics analysis. The core software performs feature detection on MS/MS data to extract ion chromatograms and determine the retention time positions of all potential fragment ions (transitions) for user-specified peptide sequences (target analytes). By learning patterns from all identified transitions within each peptide, the algorithm derives consensus start and end point of the ion chromatograms in each peptide and applies the rule during the peak integration of all its transitions. The user can easily visualize peak integration results using a custom script provided in the package. If desired, the user can manually change the integration boundaries of chosen analytes. PRMkit requires two input files: (a) table containing the peptide sequences, precursor mass-to-charge ratios, and peptide charge states, and (b) a list of mzML files pointing to all analyses. The software produces a tab-delimited output table containing peak area values for individual transitions and pdf files for the ion chromatograms across all peptides and samples.

Quantification of peptide peak area integration by PRMkit (A) Schematic of PRMkit chromatogram extraction and peak integration. (B) Example of peptide sequences, precursor m/z, and charge states required as input for PRMkit. (C) Example of PRMkit identification the uS3.K200 biological (TGPK[GG]ALPDAVTIIEPK+++) and heavy-labeled (TGPK(GG)ALPDAVTIIEPK[8.0142]+++) peptide y and b ion transitions in decreasing order of integrated peak area. Gray rectangle shows the range of integration in each window.