Peptide Charge State Determination for Low-Resolution Tandem Mass Spectra. - Aaron A. Klammer; Christine C. Wu; Michael J. MacCoss; William Stafford Noble (CSB, 2005)

Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions. - Aaron A. Klammer; Xianhua Yi; Michael J. MacCoss; William Stafford Noble (RECOMB, 2007)

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. - Aaron A. Klammer; Sheila M. Reynolds; Jeff A. Bilmes; Michael J. MacCoss; William Stafford Noble (ISMB, 2008)

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)

Estimating relative abundances of proteins from shotgun proteomics data. - Sean McIlwain; Michael Mathews; Michael Bereman; Edwin W. Rubel; Michael J. MacCoss; William Stafford Noble (BMC Bioinform., 2012)

Computational and Statistical Analysis of Protein Mass Spectrometry Data. - William Stafford Noble; Michael J. MacCoss (PLoS Comput. Biol., 2012)

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)

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)

Ripple: A Practical Declarative Programming Framework for Serverless Compute. - Shannon Joyner; Michael J. MacCoss; Christina Delimitrou; Hakim Weatherspoon (CoRR, 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)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; 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)