General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. - Brendan MacLean; Jimmy K. Eng; Ronald C. Beavis; Martin McIntosh (Bioinform., 2006)

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. - Brendan MacLean; Daniela M. Tomazela; Nicholas Shulman; Matthew Chambers; Gregory L. Finney; Barbara Frewen; Randall Kern; David L. Tabb; Daniel C. Liebler; Michael J. MacCoss (Bioinform., 2010)

A framework for installable external tools in Skyline. - Daniel Broudy; Trevor Killeen; Meena Choi; Nicholas Shulman; Deepak R. Mani; Susan E. Abbatiello; Deepak Mani; Rushdy Ahmad; Alexandria K. Sahu; Birgit Schilling; Kaipo Tamura; Yuval Boss; et al. (Bioinform., 2014)

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. - Meena Choi; Ching-Yun Chang; Timothy Clough; Daniel Broudy; Trevor Killeen; Brendan MacLean; Olga Vitek (Bioinform., 2014)

Chapter 9. Informatics Solutions for Selected Reaction Monitoring. - Birgit Schilling; Brendan MacLean; Jason M. Held; Bradford W. Gibson (Proteome Informatics, 2016)

Audit logs to enforce document integrity in Skyline and Panorama. - Tobias Rohde; Rita Chupalov; Nicholas Shulman; Vagisha Sharma; Josh Eckels; Brian S. Pratt; Michael J. MacCoss; Brendan MacLean (Bioinform., 2020)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)