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Journal of Proteome Research|May 8, 2012
Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptidesStacy D Sherrod, Matthew V Myers, Ming Li, et al.Nature Methods|November 17, 2020
Avant-garde: an automated data-driven DIA data curation toolAlvaro Sebastian Vaca Jacome, Ryan Peckner, Nicholas Shulman, et al.Biorxiv : the Preprint Server for Biology|June 19, 2024
Koina: Democratizing machine learning for proteomics researchLudwig Lautenbacher, Kevin L Yang, Tobias Kockmann, et al.Analytical Chemistry|September 24, 2015
Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric WorkflowsBirgit Schilling, Brendan MacLean, Jason M Held, et al.Journal of Proteome Research|September 27, 2022
TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling StudiesNathan Basisty, Nicholas Shulman, Cameron Wehrfritz, et al.Journal of Proteome Research|December 20, 2016
ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS ExperimentsMeena Choi, Zeynep F Eren-Dogu, Christopher Colangelo, et al.Nature Biotechnology|November 8, 2016
A multicenter study benchmarks software tools for label-free proteome quantificationPedro Navarro, Jörg Kuharev, Ludovic C Gillet, et al.Journal of Proteome Research|January 7, 2006
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experimentsAdam Rauch, Matthew Bellew, Jimmy Eng, et al.Bioinformatics (Oxford, England)|May 13, 2014
A framework for installable external tools in SkylineDaniel Broudy, Trevor Killeen, Meena Choi, et al.Nucleic Acids Research|November 9, 2025
The ProteomeXchange consortium in 2026: making proteomics data FAIREric W Deutsch, Nuno Bandeira, Yasset Perez-Riverol, et al.Pageof 4