MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

摘要: Shotgun proteomics experiments require the collection of thousands tandem mass spectra; these sets data will continue to grow as new instruments become available that can scan at even higher rates. Such contain substantial amounts redundancy with spectra from a particular peptide being acquired many times during single LC-MS/MS experiment. In this article, we present MS2Grouper, an algorithm detects spectral duplication, assesses groups related spectra, and replaces synthetic representative spectra. Errors in detecting similarity are corrected using paraclique criterion—spectra only assessed if they part clique least three completely interrelated or subsequently added such cliques by similar all but one members. A greedy constructs spectrum for each group iteratively removing tallest peaks matching other This strategy is shown be effective reducing counts up 20% datasets protein standard mixtures proteomes, database search without concomitant reduction identified peptides.