quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data
Chengxin Dai, Julianus Pfeuffer, Hong Wang, Ping Zheng, Lukas Käll, Timo Sachsenberg, Vadim Demichev, Mingze Bai, Oliver Kohlbacher, Yasset Pérez‐Riverol
Abstract
The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms ( https://quant,ms.org/ ), an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 83 public ProteomeXchange datasets, comprising 29,354 instrument files from 13,132 human samples, to quantify 16,599 proteins based on 1.03 million unique peptides. quantms is based on standard file formats improving the reproducibility, submission and dissemination of the data to ProteomeXchange.
Topics & Concepts
ProteomicsCloud computingPipeline (software)Computational biologyQuantitative proteomicsComputer scienceData scienceBiologyGeneBiochemistryProgramming languageOperating systemAdvanced Proteomics Techniques and ApplicationsScientific Computing and Data ManagementGenetics, Bioinformatics, and Biomedical Research