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 […]
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Group Members

Grigory Reznikov

General Member

Majid Mohammadi

General Member

2026

Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry

Austin Z. Salome, Marcel Morgenstern, Alexander S. Hebert, Craig D. Wenger, Pavel Sinitcyn, Benton J. Anderson, John S. Chlystek, Lia R. Serrano, Keaton L. Mertz, Ian Miller, Erik Miller-Galow, Malika P Godamudunage, Michael Batt, Bhavin 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)

Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks

Grigory Reznikov, Fabrice Kusters, Majid Mohammadi, Henk W.P. van den Toorn, Pavel Sinitcyn

bioRxiv (Cold Spring Harbor Laboratory)

AI‐driven antibody design from an antigen sequence

Pavel Sinitcyn, Albert J. R. Heck

Vita

2025

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 Sinitcyn, Anand Patel, Natalie Castellana, Stefano Bonissone, Stian Foss, Jan Terje Andersen, Geir Kjetil Sandve, Timothy P. Jenkins, William Stafford Noble, Tuula A. Nyman, Igor Snapkov, Victor Greiff

Cell Systems

Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition

Keaton L. Mertz, Lia R. Serrano, Pavel Sinitcyn, Joshua J. Coon

Journal of the American Society for Mass Spectrometry

From reference to reality: identifying noncanonical peptides

Ellen Frances Shute, Pavel Sinitcyn

Trends in Genetics

Technical Evaluation of Plasma Proteomics Technologies

William F. Beimers, Katherine A. Overmyer, Pavel Sinitcyn, Noah M. Lancaster, Scott T. Quarmby, Joshua J. Coon

Journal of Proteome Research

Abstract 1356 Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral

Noah M. Lancaster, Pavel Sinitcyn, Patrick Forny, David J. Pagliarini, Vlad Zabrouskov, Joshua J. Coon

Journal of Biological Chemistry

Deep Learning Predicts Non-Normal Transmission Distributions in High-Field Asymmetric Waveform Ion Mobility (FAIMS) Directly from Peptide Sequence

Justin McKetney, Ian Miller, A. Hutton, Pavel Sinitcyn, Lia R. Serrano, Joshua J. Coon, Jesse G. Meyer

Analytical Chemistry

2024

Deep Learning Predicts Non-Normal Peptide FAIMS Mobility Distributions Directly from Sequence

Justin McKetney, Ian Miller, A. Hutton, Pavel Sinitcyn, Joshua J. Coon, Jesse G. Meyer

bioRxiv (Cold Spring Harbor Laboratory)Preprint

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

Noah M. Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M. Peters-Clarke, Caroline Fecher, Andrew J. H. Smith, Evgenia Shishkova, Tabiwang N. Arrey, Anna Pashkova, Margaret Lea Robinson, Nicholas L. Arp, Jing Fan, J N Hansen, Andrea Galmozzi, Lia R. Serrano, Julie Rojas, Audrey P. Gasch, Michael S. Westphall, Hamish Stewart, Christian Hock, Eugen Damoc, David J. Pagliarini, Vlad Zabrouskov, Joshua J. Coon

Nature Communications

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, C. Moss, Anna Pashkova, Pavel Sinitcyn, Dain R. Brademan, Scott T. Quarmby, Amelia C. Peterson, Martin Zeller, Daniel Hermanson, Hamish Stewart, Christian Hock, Alexander Makarov, Vlad Zabrouskov, Joshua J. Coon

Molecular & Cellular Proteomics

2023

Deep and fast label-free Dynamic Organellar Mapping

Julia P. Schessner, Vincent Albrecht, Alexandra K. Davies, Pavel Sinitcyn, Georg H. H. Borner

Nature Communications

Global detection of human variants and isoforms by deep proteome sequencing

Pavel Sinitcyn, Alicia Richards, Robert J. Weatheritt, Dain R. Brademan, Harald Marx, Evgenia Shishkova, Jesse G. Meyer, Alexander S. Hebert, Michael S. Westphall, Benjamin J. Blencowe, Jürgen Cox, Joshua J. Coon

Nature Biotechnology

Multi-targeted therapy resistance via drug-induced secretome fucosylation

Mark Borris D. Aldonza, Junghwa Cha, Insung Yong, Jayoung Ku, Pavel Sinitcyn, Dabin Lee, Ryeong-Eun Cho, Roben Delos Reyes, Dongwook Kim, Soyeon Kim, Minjeong Kang, Yongsuk Ku, Geonho Park, Hye-Jin Sung, Han Suk Ryu, Sukki Cho, Tae Min Kim, Pilnam Kim, Je‐Yoel Cho, Yoosik Kim

eLife

View Pavel Sinitcyn on ORCID →