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The package mms2plot visualizes multiple tandem mass spectrometry (MS/MS or MS2) for modificated and/or non-modified peptides identified from the same raw MS files, annotated by peptide identification algorithms. It will output a mirror-style plots for two peptide-spectrum matches (PSMs) and an aligned plot for more than two PSMs. MMS2plot features a batch mode and generates the output images in vector graphics file format (i.e. PDF) that facilitate evaluation and publication of the PSM assignment.The output file width is recommended as 3.35 inch (single column) or 7 inch (double column).

NOte: If you fail to install mms2plot on Windows OS, please install it by re-running R or RStudio with admin rights.

MMS2plot user guide is included as well as a packed example of MMS2plot required files as Supplemenary file 1.

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Visualization of multiple tandem mass spectrometry data

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