Author

Peter R. Baker

University of California, San FranciscoORCID 0000-0001-7826-9251Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:proteomics· 2 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Research Focus:software / tool· 1 Approach:statistical model· 1

Frequent Co-Authors

Robert J. ChalkleyiD· 2 shared Alma L. BurlingameiD· 1 shared Andrew CollinsiD· 1 shared Clinton YuiD· 1 shared Emanuele AlpiiD· 1 shared Eric W. DeutschiD· 1 shared Eugene A. KappiD· 1 shared Fenglong JiaoiD· 1 shared

Activity by Year

2019-2026 · peak 1/yr

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10 top collaborators · 27 mutual co-author links

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2 shared papersBioinformatics

Robert J. ChalkleyORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 15, 2026

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

Michael J. Trnka, Clinton Yu, Peter R. Baker…·Lan Huang

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

DOI 10.64898/2026.10.08.757733

proteomicsstatistical model

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BioinformaticsJournal of Proteome ResearchPeer-reviewedMay 13, 2019

Proteomics Standards Initiative Extended FASTA Format (PEFF)

Pierre‐Alain Binz, Jim Shofstahl, Juan Antonio Vizcaíno…·Eric W. Deutsch

The paper introduces PEFF, a new format for proteomics data that enhances FASTA with metadata for sequence variants and PTMs, enabling better analysis in proteogenomics and top-down proteomics.

34 citations

proteomicsdatabase / resource

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