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Published on: October 28, 2021
ProtyQuant: A Step-by-Step Protocol for Label-Free Protein Quantification in Data-Dependent Acquisition (DDA) Shotgun
1Advanced Genomics Unit (UGA), Center for Research and Advanced Studies (Cinvestav) Irapuato, Kilómetro 9.6, Carretera Libramiento Irapuato-León, Irapuato, Gto., 36824, Mexico. robert.winkler@cinvestav.mx.
Abstract:
This chapter explains how to use ProtyQuant software to do label-free protein quantification in data-dependent acquisition (DDA) shotgun proteomics. Using the innovative "accumulated peptide probabilities" (APP) metric, it unifies protein inference and quantification, addressing significant issues in conventional workflows. The protocol gives a step-by-step guide that starts with preparing raw mass spectrometry data and searching databases. It then moves on to validating peptides and ends with using ProtyQuant to infer proteins and estimate their amounts. It further outlines the optional postprocessing analysis using R. Emphasizing reproducibility and accessibility, the entire workflow is integrated within MASSyPupX, a free and open-source Linux distribution, enabling researchers to perform high-throughput proteomics studies efficiently from a portable USB drive. This guide is designed to empower researchers in academic, clinical, and industrial settings to generate statistically robust and interpretable protein abundance data.MASSyPupX can be accessed via Zenodo ( https://doi.org/10.5281/zenodo.14618430 ) and its project page ( https://codeberg.org/LabABI/MASSyPupX ).
