Author

Dmitry M. Avtonomov

University of MichiganORCID 0000-0002-8758-3901Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Assay:proteomics· 3 Approach:statistical model· 3 Approach:experimental assay· 2 Research Focus:software / tool· 2 Research Focus:variant calling· 2 Research Focus:database / resource· 1 Organism:E. coli· 1

Frequent Co-Authors

Alexey I. NesvizhskiiiD· 3 shared Fengchao YuiD· 3 shared Felipe da Veiga LeprevostiD· 2 shared Sarah E. HaynesiD· 2 shared Andy T. KongiD· 1 shared Bing ZhangiD· 1 shared Bo WeniD· 1 shared Daniel A. PolaskyiD· 1 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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3 shared papersBioinformatics

Alexey I. NesvizhskiiORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform

Hui-Yin Chang, Yamei Deng, Ruohong Li, Dmitry M. Avtonomov, Bo Wen, Sarah Haynes, Felipe da Veiga Leprevost, Bing Zhang, Fengchao Yu, Alexey I. Nesvizhskii

The paper introduces TMT-Integrator, a tool for analyzing isobaric proteomic data, showing improved performance in protein and phosphorylation site quantification compared to existing tools.

Nature Communications · Mar 2, 2026Peer-reviewedBioinformatics

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

Daniel Geiszler, Andy T. Kong, Dmitry M. Avtonomov, Fengchao Yu, Felipe da Veiga Leprevost, Alexey I. Nesvizhskii

PTM-Shepherd automates analysis of post-translational modifications from open search proteomics data, improving detection of artifacts and biases across experiments.

Molecular & Cellular Proteomics · Dec 1, 2020Peer-reviewedBioinformatics

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

Fengchao Yu, Sarah E. Haynes, Guo Ci Teo, Dmitry M. Avtonomov, Daniel A. Polasky, Alexey I. Nesvizhskii

The paper introduces MSFragger and IonQuant for fast analysis of timsTOF PASEF data, showing improved peptide identification and quantification compared to existing tools.

Molecular & Cellular Proteomics · Jul 2, 2020Peer-reviewedBioinformatics