Group

The people behind the University of Washington's Proteomics Resource

The UWPR proteomics informatics group is a University of Washington team that develops open-source software and computational methods for mass spectrometry–based proteomics, and provides data-analysis support to the University of Washington's Proteomics Resource. Tools originating from group members — including SEQUEST, the Trans-Proteomic Pipeline, Comet, Skyline, Kojak, Panorama, and Osprey — are used by proteomics laboratories worldwide and have been cited in tens of thousands of publications. The group's own research is documented on the Resource's publications page, which lists work supported by the UWPR going back over a decade.

MH

Michael R. Hoopmann, PhD — Principal Investigator / Group Leader

Senior Research Scientist, Department of Genome Sciences · University of Washington Proteomics Resource

Michael Hoopmann leads the group's software and computational method development. A former Senior Research Scientist at the Institute for Systems Biology, he joined the University of Washington full-time in 2024. He is the primary developer of Kojak, a widely used search engine for cross-linking mass spectrometry, and is a core contributor to the Comet search engine, the Trans-Proteomic Pipeline (TPP), and instrument-control software used throughout the field. He serves as Co-Chair of the ABRF Proteome Informatics Research Group (iPRG) and is the primary technical contact for UWPR instrumentation and data-analysis questions. His work has been cited more than 7,200 times (h-index 42).

ORCID Google Scholar Schweppe Lab profile hoopmann@uw.edu

Group Members

JE

Jimmy Eng

Jimmy Eng originally developed SEQUEST, the first widely adopted algorithm for matching tandem mass spectra to peptide sequences in a protein database, and later created its open-source successor Comet. He is a longtime contributor to the Trans-Proteomic Pipeline and supports data analysis for the UWPR. His work has been cited more than 50,000 times (h-index 89).

ORCID Google Scholar engj@uw.edu

VS

Vagisha Sharma

Vagisha Sharma is a core developer of the Skyline targeted-proteomics ecosystem, including its external-tools framework, Skyline Batch, and the Panorama document repository, and is an active contributor to the international ProteomeXchange consortium for proteomics data sharing. She supports software and data-analysis questions for the UWPR.

ORCID vsharma@uw.edu

VG

Veronika Glukova

Veronika Glukova supports the Resource's lab and operations activities, helping coordinate the sample and instrument workflows that keep the group's proteomics facility and research running day to day.

spionin@uw.edu

MR

Michael Riffle

Mike Riffle is a Senior Computer Specialist developing bioinformatics tools for data-independent-acquisition proteomics (including Osprey), methods for false-discovery-rate control via entrapment analysis, and MetaGOmics, a web tool for functional and taxonomic analysis of metaproteomics data. His work has been cited more than 3,800 times (h-index 30).

ORCID Google Scholar riffle@uw.edu

Selected Publications

Each member's most-cited work as first author

The Resource's publications page tracks papers directly supported by UWPR instrumentation and staff time. It does not capture the group's full body of research, so a few of each member's most-cited papers as first author are listed below.

Michael Hoopmann

  • Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL. Kojak: efficient analysis of chemically cross-linked protein complexes. J Proteome Res. 2015;14(5):2190-2198. PubMed — ~230 citations
  • Hoopmann MR, Finney GL, MacCoss MJ. High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal Chem. 2007;79(15):5620-5632. PubMed — ~200 citations
  • Hoopmann MR, Winget JM, Mendoza L, Moritz RL. StPeter: Seamless label-free quantification with the Trans-Proteomic Pipeline. J Proteome Res. 2018;17(3):1314-1320. PubMed — ~25 citations

Jimmy Eng

  • Eng JK, McCormack AL, Yates JR 3rd. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom. 1994;5(11):976-989. DOI — ~8,600 citations (the original SEQUEST paper)
  • Eng JK, Jahan TA, Hoopmann MR. Comet: an open-source MS/MS sequence database search tool. Proteomics. 2013;13(1):22-24. PubMed — ~1,900 citations
  • Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ. A deeper look into Comet—implementation and features. J Am Soc Mass Spectrom. 2015;26(11):1865-1874. PubMed — ~340 citations

Vagisha Sharma

  • Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B. Panorama: a targeted proteomics knowledge base. J Proteome Res. 2014;13(9):4205-4210. PubMed — ~210 citations
  • Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B. Panorama Public: a public repository for quantitative data sets processed in Skyline. Mol Cell Proteomics. 2018;17(6):1239-1244. PubMed — ~200 citations

Michael Riffle

  • Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL. MetaGOmics: a web-based tool for peptide-centric functional and taxonomic analysis of metaproteomics data. Proteomes. 2017;6(1):2. PubMed — ~40 citations
  • Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A. Discovery and visualization of uncharacterized drug–protein adducts using mass spectrometry. Anal Chem. 2022;94(8):3501-3509. PubMed — ~20 citations

See the Resource's full publications list, software and tools, and contact information for more about the group's work.