We develop open, reproducible methods for computational mass spectrometry.
Highlighted Publications
Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer
N. M. Lancaster, P. Sinitcyn, P. Forny, et al.
Nature Communications 2024 [Link]
N. M. Lancaster, P. Sinitcyn, P. Forny, et al.
Nature Communications 2024 [Link]
- Unlocks deep phosphoproteome coverage (over 30,000 phosphosites) in short gradients.
- Demonstrates high-throughput capability for large-scale signaling studies in mouse tissues.
- Establishes benchmarks for the new Orbitrap Astral technology.
Global detection of human variants and isoforms by deep proteome sequencing
P. Sinitcyn, A. L. Richards, et al.
Nature Biotechnology 2023 [Link]
P. Sinitcyn, A. L. Richards, et al.
Nature Biotechnology 2023 [Link]
- Directly detects single amino acid variants and alternative isoforms at the protein level.
- Integrates genomic, transcriptomic, and proteomics data for comprehensive proteogenomics.
MaxDIA enables library-based and library-free data-independent acquisition proteomics
P. Sinitcyn, H. Hamzeiy, F. Salinas Soto, et al.
Nature Biotechnology 2021 [Link]
P. Sinitcyn, H. Hamzeiy, F. Salinas Soto, et al.
Nature Biotechnology 2021 [Link]
- Introduces MaxDIA for robust analysis of Data-Independent Acquisition (DIA) data.
- Enables both spectral library-based and library-free (discovery) workflows.
- Improves identification accuracy and quantification precision in complex samples.
All Publications
Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases
M. Chernigovskaya, K. Lê Quý, M. Stensland, S. Singh, R. Nelson, M. Yilmaz, K. Kalogeropoulos, P. Sinitcyn, A. Patel, N. Castellana, S. Bonissone, S. Foss, J. T. Andersen, G. K. Sandve, T. P. Jenkins, W. S. Noble, T. A. Nyman, I. Snapkow, V. Greiff
Cell Systems 2025 [Link]
M. Chernigovskaya, K. Lê Quý, M. Stensland, S. Singh, R. Nelson, M. Yilmaz, K. Kalogeropoulos, P. Sinitcyn, A. Patel, N. Castellana, S. Bonissone, S. Foss, J. T. Andersen, G. K. Sandve, T. P. Jenkins, W. S. Noble, T. A. Nyman, I. Snapkow, V. Greiff
Cell Systems 2025 [Link]
From reference to reality: identifying noncanonical peptides
E. F. Shute, P. Sinitcyn
Trends in Genetics 2025 [Link]
E. F. Shute, P. Sinitcyn
Trends in Genetics 2025 [Link]
Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition
K. L. Mertz, L. R. Serrano, P. Sinitcyn, J. J. Coon
Journal of the American Society for Mass Spectrometry 2025 [Link]
K. L. Mertz, L. R. Serrano, P. Sinitcyn, J. J. Coon
Journal of the American Society for Mass Spectrometry 2025 [Link]
Technical Evaluation of Plasma Proteomics Technologies
W. F. Beimers, K. A. Overmyer, P. Sinitcyn, N. M. Lancaster, S. T. Quarmby, J. J. Coon
Journal of Proteome Research 2025 [Link]
W. F. Beimers, K. A. Overmyer, P. Sinitcyn, N. M. Lancaster, S. T. Quarmby, J. J. Coon
Journal of Proteome Research 2025 [Link]
Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer
N. M. Lancaster, P. Sinitcyn, P. Forny, T. M. Peters-Clarke, C. Fecher, A. J. Smith, E. Shishkova, T. N. Arrey, A. Pashkova, M. L. Robinson, N. Arp, J. Fan, J. Hansen, A. Galmozzi, L. R. Serrano, J. Rojas, A. P. Gasch, M. S. Westphall, H. Stewart, C. Hock, E. Damoc, D. J. Pagliarini, V. Zabrouskov, J. J. Coon
Nature Communications 2024 [Link]
N. M. Lancaster, P. Sinitcyn, P. Forny, T. M. Peters-Clarke, C. Fecher, A. J. Smith, E. Shishkova, T. N. Arrey, A. Pashkova, M. L. Robinson, N. Arp, J. Fan, J. Hansen, A. Galmozzi, L. R. Serrano, J. Rojas, A. P. Gasch, M. S. Westphall, H. Stewart, C. Hock, E. Damoc, D. J. Pagliarini, V. Zabrouskov, J. J. Coon
Nature Communications 2024 [Link]
The One Hour Human Proteome
L. R. Serrano, T. M. Peters-Clarke, T. N. Arrey, E. Damoc, M. L. Robinson, N. M. Lancaster, E. Shishkova, C. Moss, A. Pashkova, P. Sinitcyn, D. R. Brademan, S. T. Quarmby, A. C. Peterson, M. Zeller, D. Hermanson, H. Stewart, C. Hock, A. Makarov, V. Zabrouskov, J. J. Coon
Molecular & Cellular Proteomics 2024 [Link]
L. R. Serrano, T. M. Peters-Clarke, T. N. Arrey, E. Damoc, M. L. Robinson, N. M. Lancaster, E. Shishkova, C. Moss, A. Pashkova, P. Sinitcyn, D. R. Brademan, S. T. Quarmby, A. C. Peterson, M. Zeller, D. Hermanson, H. Stewart, C. Hock, A. Makarov, V. Zabrouskov, J. J. Coon
Molecular & Cellular Proteomics 2024 [Link]
Deep and fast label-free Dynamic Organellar Mapping
J. P. Schessner, V. Albrecht, A. K. Davies, P. Sinitcyn, G. H. H. Borner
Nature Communications 2023 [Link]
J. P. Schessner, V. Albrecht, A. K. Davies, P. Sinitcyn, G. H. H. Borner
Nature Communications 2023 [Link]
Multi-targeted therapy resistance via drug-induced secretome fucosylation
M. B. D. Aldonza, J. Cha, I. Yong, J. Ku, P. Sinitcyn, D. Lee, R-E. Cho, R. D. Delos Reyes, D. Kim, S. Kim, M. Kang, Y. Ku, G. Park, H-J. Sung, H. S. Ryu, S. Cho, T. M. Kim, P. Kim, J-Y. Cho, Y. Kim
eLife 2023 [Link]
M. B. D. Aldonza, J. Cha, I. Yong, J. Ku, P. Sinitcyn, D. Lee, R-E. Cho, R. D. Delos Reyes, D. Kim, S. Kim, M. Kang, Y. Ku, G. Park, H-J. Sung, H. S. Ryu, S. Cho, T. M. Kim, P. Kim, J-Y. Cho, Y. Kim
eLife 2023 [Link]
Global detection of human variants and isoforms by deep proteome sequencing
P. Sinitcyn, A. L. Richards, R. J. Weatheritt, D. R. Brademan, H. Marx, E. Shishkova, J. G. Meyer, A. S. Hebert, M. S. Westphall, B. J. Blencowe, J. Cox, J. J. Coon
Nature Biotechnology 2023 [Link]
P. Sinitcyn, A. L. Richards, R. J. Weatheritt, D. R. Brademan, H. Marx, E. Shishkova, J. G. Meyer, A. S. Hebert, M. S. Westphall, B. J. Blencowe, J. Cox, J. J. Coon
Nature Biotechnology 2023 [Link]
MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides
P. Sinitcyn, M. Gerwien, J. Cox
Methods in Molecular Biology 2022 [Link]
P. Sinitcyn, M. Gerwien, J. Cox
Methods in Molecular Biology 2022 [Link]
Progress and challenges in mass spectrometry-based analysis of antibody repertoires
I. Snapkov, M. Chernigovskaya, P. Sinitcyn, K. Lê Quý, T. A. Nyman, V. Greiff
Trends in Biotechnology 2022 [Link]
I. Snapkov, M. Chernigovskaya, P. Sinitcyn, K. Lê Quý, T. A. Nyman, V. Greiff
Trends in Biotechnology 2022 [Link]
MaxDIA enables library-based and library-free data-independent acquisition proteomics
P. Sinitcyn, H. Hamzeiy, F. Salinas Soto, D. Itzhak, F. McCarthy, C. Wichmann, M. Steger, U. Ohmayer, U. Distler, S. Kaspar-Schoenefeld, N. Prianichnikov, Ş. Yılmaz, J. D. Rudolph, S. Tenzer, Y. Perez-Riverol, N. Nagaraj, S. J. Humphrey, J. Cox
Nature Biotechnology 2021 [Link]
P. Sinitcyn, H. Hamzeiy, F. Salinas Soto, D. Itzhak, F. McCarthy, C. Wichmann, M. Steger, U. Ohmayer, U. Distler, S. Kaspar-Schoenefeld, N. Prianichnikov, Ş. Yılmaz, J. D. Rudolph, S. Tenzer, Y. Perez-Riverol, N. Nagaraj, S. J. Humphrey, J. Cox
Nature Biotechnology 2021 [Link]
Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains
D. S. Makeeva, A. S. Lando, A. Anisimova, A. A. Egorov, M. D. Logacheva, A. A. Penin, D. E. Andreev, P. G. Sinitcyn, I. M. Terenin, I. N. Shatsky, I. V. Kulakovskiy, S. E. Dmitriev
Data in Brief 2019 [Link]
D. S. Makeeva, A. S. Lando, A. Anisimova, A. A. Egorov, M. D. Logacheva, A. A. Penin, D. E. Andreev, P. G. Sinitcyn, I. M. Terenin, I. N. Shatsky, I. V. Kulakovskiy, S. E. Dmitriev
Data in Brief 2019 [Link]
A novel uORF-based regulatory mechanism controls translation of the human MDM2 and eIF2D mRNAs during stress
K. A. Akulich, P. G. Sinitcyn, D. S. Makeeva, D. E. Andreev, I. M. Terenin, A. S. Anisimova, I. N. Shatsky, S. E. Dmitriev
Biochimie 2019 [Link]
K. A. Akulich, P. G. Sinitcyn, D. S. Makeeva, D. E. Andreev, I. M. Terenin, A. S. Anisimova, I. N. Shatsky, S. E. Dmitriev
Biochimie 2019 [Link]
The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins
M. J. Shurtleff, D. N. Itzhak, J. A. Hussmann, N. T. Schirle Oakdale, E. A. Costa, M. Jonikas, J. Weibezahn, K. D. Popova, C. H. Jan, P. Sinitcyn, S. S. Vembar, H. Hernandez, J. Cox, A. L. Burlingame, J. L. Brodsky, A. Frost, G. H. Borner, J. S. Weissman
eLife 2018 [Link]
M. J. Shurtleff, D. N. Itzhak, J. A. Hussmann, N. T. Schirle Oakdale, E. A. Costa, M. Jonikas, J. Weibezahn, K. D. Popova, C. H. Jan, P. Sinitcyn, S. S. Vembar, H. Hernandez, J. Cox, A. L. Burlingame, J. L. Brodsky, A. Frost, G. H. Borner, J. S. Weissman
eLife 2018 [Link]
Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data
P. Sinitcyn, J. D. Rudolph, J. Cox
Annual Review of Biomedical Data Science 2018 [Link]
P. Sinitcyn, J. D. Rudolph, J. Cox
Annual Review of Biomedical Data Science 2018 [Link]
MaxQuant goes Linux
P. Sinitcyn, S. Tiwary, J. Rudolph, P. Gutenbrunner, C. Wichmann, Ş. Yılmaz, H. Hamzeiy, F. Salinas, J. Cox
Nature Methods 2018 [Link]
P. Sinitcyn, S. Tiwary, J. Rudolph, P. Gutenbrunner, C. Wichmann, Ş. Yılmaz, H. Hamzeiy, F. Salinas, J. Cox
Nature Methods 2018 [Link]
Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry
M. Bassani-Sternberg, E. Bräunlein, R. Klar, T. Engleitner, P. Sinitcyn, S. Audehm, M. Straub, J. Weber, J. Slotta-Huspenina, K. Specht, M. E. Martignoni, A. Werner, R. Hein, D. H. Busch, C. Peschel, R. Rad, J. Cox, M. Mann, A. M. Krackhardt
Nature Communications 2016 [Link]
M. Bassani-Sternberg, E. Bräunlein, R. Klar, T. Engleitner, P. Sinitcyn, S. Audehm, M. Straub, J. Weber, J. Slotta-Huspenina, K. Specht, M. E. Martignoni, A. Werner, R. Hein, D. H. Busch, C. Peschel, R. Rad, J. Cox, M. Mann, A. M. Krackhardt
Nature Communications 2016 [Link]
The Perseus computational platform for comprehensive analysis of (prote)omics data
S. Tyanova, T. Temu, P. Sinitcyn, A. Carlson, M. Y. Hein, T. Geiger, M. Mann, J. Cox
Nature Methods 2016 [Link]
S. Tyanova, T. Temu, P. Sinitcyn, A. Carlson, M. Y. Hein, T. Geiger, M. Mann, J. Cox
Nature Methods 2016 [Link]
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
N. Grassl, N. A. Kulak, G. Pichler, P. E. Geyer, J. Jung, S. Schubert, P. Sinitcyn, J. Cox, M. Mann
Genome Medicine 2016 [Link]
N. Grassl, N. A. Kulak, G. Pichler, P. E. Geyer, J. Jung, S. Schubert, P. Sinitcyn, J. Cox, M. Mann
Genome Medicine 2016 [Link]
Visualization of LC‐MS/MS proteomics data in MaxQuant
S. Tyanova, T. Temu, A. Carlson, P. Sinitcyn, M. Mann, J. Cox
PROTEOMICS 2015 [Link]
S. Tyanova, T. Temu, A. Carlson, P. Sinitcyn, M. Mann, J. Cox
PROTEOMICS 2015 [Link]