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BioMS

Biomolecular Mass Spectrometry
and proteomics

Sinitcyn Lab

Pavel Sinitcyn

Assistant Professor

Pavel works as an Assistant Professor in AI Technology for Life (Department of Information and Computing Sciences) and Biomolecular Mass Spectrometry and Proteomics (Department of Pharmaceutical Sciences) groups at Utrecht University. My research focuses on computational methods for analyzing mass spectrometry-based proteomics data, including advanced machine learning techniques.

Awarded Grants

There are currently no awards noted down.

Group News

  • QuadraSHAP Featured by Nebius Science

    June 7, 2026

    Nebius Science featured our recent work on QuadraSHAP – a fast and numerically stable algorithm for computing Shapley values. Shapley values are a popular framework for explaining machine learning models, but their factorial computational cost makes them prohibitively slow in practice. Majid Mohammadi worked out the key theoretical insight – the painful sum over feature coalitions […]

    Read more →

Group Members

Grigory Reznikov

General Member

Majid Mohammadi

General Member

2026

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Disentangling maternal pregnancy and fetal-specific plasma signatures through integrated proteomics and site-specific N-glycoproteomics
Shelley Jager, Sofia Kalaidopoulou Nteak, Grigory Reznikov, Francine R. Ianiski, Remco Visser, Pavel G. Sinitcyn, Gestur Vidarsson, Albert J. R. Heck
bioRxiv (Cold Spring Harbor Laboratory)Preprint
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Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks
Grigory Reznikov, Fabrice Kusters, Majid Mohammadi, Henk van den Toorn, Pavel G. Sinitcyn
Journal of Proteome Research
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Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members
Dirk Winkelhardt, Julia Patricia Schessner, Sven Berres, Alireza Nameni, Armin Soleymaniniya, Ayla Schröder, Caroline Jachmann, Douwe Schulte, Georg Wallmann, Henry Emanuel Webel, Johannes Rainer, Katerina Nastou, Laurent Gatto, Magnus Palmblad, Maike Weber, Omar Osama Shouman, Pavel G. Sinitcyn, Ralf Gabriels, Robbe Devreese, Tim Van Den Bossche, Tine Claeys, Wout Bittremieux, Julian Uszkoreit
Journal of Proteomics
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Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry
Austin Z. Salome, Marcel Morgenstern, Alexander S. Hebert, Craig D. Wenger, Pavel G. Sinitcyn, Benton J. Anderson, John S. Chlystek, Lia R. Serrano, Keaton L. Mertz, Ian J. Miller, Erik Miller-Galow, Malika P. Godamudunage, Michael Batt, Bhavin R. Patel, Gihoon Lee, Lloyd M. Smith, Scott T. Quarmby, Alayna M. George Thompson, Joomi Ahn, Harsha P. Gunawardena, Joshua J. Coon
bioRxiv (Cold Spring Harbor Laboratory)Preprint
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QuadraSHAP: $ε$-Exact Shapley Values for Product Games in Logarithmic Parallel Time
Majid Mohammadi, Grigory Reznikov, Pavel G. Sinitcyn, Krikamol Muandet, Siu Lun Chau
arXiv (Cornell University)Preprint
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AI‐driven antibody design from an antigen sequence
Pavel G. Sinitcyn, Albert J. R. Heck
Vita

2025

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Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
Maria Chernigovskaya, Khang Lê Quý, Maria Stensland, Sachin Kumar Singh, Rowan Nelson, Melih Yilmaz, Konstantinos Kalogeropoulos, Pavel G. Sinitcyn, Anand D. Patel, Natalie E. Castellana, Stefano R. Bonissone, Stian Foss, Jan Terje Andersen, Geir Kjetil Sandve, Timothy P. Jenkins, William Stafford Noble, Tuula A. Nyman, Igor Snapkov, Victor Greiff
Cell Systems
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Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition
Keaton L. Mertz, Lia R. Serrano, Pavel G. Sinitcyn, Joshua J. Coon
Journal of the American Society for Mass Spectrometry
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From reference to reality: identifying noncanonical peptides
Ellen Frances Shute, Pavel G. Sinitcyn
Trends in Genetics
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Technical Evaluation of Plasma Proteomics Technologies
William F. Beimers, Katherine A. Overmyer, Pavel G. Sinitcyn, Noah M. Lancaster, Scott T. Quarmby, Joshua J. Coon
Journal of Proteome Research
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Deep Learning Predicts Non-Normal Transmission Distributions in High-Field Asymmetric Waveform Ion Mobility (FAIMS) Directly from Peptide Sequence
Justin McKetney, Ian J. Miller, Alexandre Hutton, Pavel G. Sinitcyn, Lia R. Serrano, Joshua J. Coon, Jesse G. Meyer
Analytical Chemistry

2024

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Deep Learning Predicts Non-Normal Peptide FAIMS Mobility Distributions Directly from Sequence
Justin McKetney, Ian J. Miller, Alexandre Hutton, Pavel G. Sinitcyn, Joshua J. Coon, Jesse G. Meyer
bioRxiv (Cold Spring Harbor Laboratory)Preprint
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Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer
Noah M. Lancaster, Pavel G. Sinitcyn, Patrick Forny, Trenton M. Peters-Clarke, Caroline Fecher, Andrew J. Smith, Evgenia Shishkova, Tabiwang N. Arrey, Anna Pashkova, Margaret Lea Robinson, Nicholas L. Arp, Jing Fan, Juli Hansen, Andrea Galmozzi, Lia R. Serrano, Julie Rojas, Audrey P. Gasch, Michael S. Westphall, Hamish I. Stewart, Christian Hock, Eugen Damoc, David J. Pagliarini, Vlad Zabrouskov, Joshua J. Coon
Nature Communications
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The One Hour Human Proteome
Lia R. Serrano, Trenton M. Peters-Clarke, Tabiwang N. Arrey, Eugen Damoc, Margaret Lea Robinson, Noah M. Lancaster, Evgenia Shishkova, Corinne E. Moss, Anna Pashkova, Pavel G. Sinitcyn, Dain R. Brademan, Scott T. Quarmby, Amelia C. Peterson, Martin Zeller, Daniel J. Hermanson, Hamish I. Stewart, Christian Hock, Alexander Makarov, Vlad Zabrouskov, Joshua J. Coon
Molecular & Cellular Proteomics

2023

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Deep and fast label-free Dynamic Organellar Mapping
Julia Patricia Schessner, Vincent Albrecht, Alexandra K. Davies, Pavel G. Sinitcyn, Georg H. H. Borner
Nature Communications

View Pavel Sinitcyn on ORCID →