MS²Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0

Abstract

Rescoring of peptide−spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We introduce MS 2 Rescore 3.0, a versatile, modular, and userfriendly platform designed to increase peptide identifications. Researchers can install MS 2 Rescore across various platforms with minimal effort and benefit from a graphical user interface, a modular Python API, and extensive documentation. To showcase this new version, we connected MS 2 Rescore 3.0 with MS Amanda 3.0, a new release of the well-established search engine, addressing previous limitations on automatic rescoring. Among new features, MS Amanda now contains additional output columns that can be used for rescoring. The full potential of rescoring is best revealed when applied on challenging data sets. We therefore evaluated the performance of these two tools on publicly available single-cell data sets, where the number of PSMs was substantially increased, thereby demonstrating that MS 2 Rescore offers a powerful solution to boost peptide identifications. MS 2 Rescore's modular design and user-friendly interface make data-driven rescoring easily accessible, even for inexperienced users. We therefore expect the MS 2 Rescore to be a valuable tool for the wider proteomics community. MS 2 Rescore is available at https://github.com/compomics/ms2rescore.

Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification

“…, delta RT, utilizing DeepLC ( 21 ). In the latest version of MS2Rescore ( 83 ), a CCS/IM predictor termed ionmob ( 84 ) was integrated that is used to generate new features scoring the difference between the expected and the observed CCS/IM of a peptide. The resulting set of data-driven features is then combined with the DBSE features ( e.g.…”

Celebrating Women in Proteomics and Metabolomics

“…As the continuous developments in sample preparation and mass spectrometry instrumentation have afforded the acquisition of proteomics and metabolomics data sets with improved depth and quality, effort has been also placed on the development of computational platforms and software required for the analysis of these increasingly complex data sets. This is well represented in this Special Issue, with papers introducing software for assessing the quality of cross-linking mass spectrometry data (RawVegetable 2.0 by Louise Ulrich Kurt and colleagues from the Costa Carvalho group), an open-source R package for relative quantification of positional isomers ( IsoForma from the Aivett Bilbao group), and a computational platform for improving peptide identification from the rescoring of peptide-spectrum matches (MS 2 Rescore 3.0 by Louie Buur and colleagues) . The Special issue also presents web-based tools for analyzing N-glycocapture data (Veneer from the Rebekah Gundry group) and for analyzing proteomics, metabolomics, lipidomics, and transcriptomics data (PMart by Kelly Stratton from Lisa Bramer’s group) .…”