Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine
Teo, Guo Ci, Polasky, Daniel A, Yu, Fengchao, Nesvizhskii, Alexey I
Published in Journal of proteome research (01.01.2021)
Published in Journal of proteome research (01.01.2021)
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Journal Article
Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides
Geiszler, Daniel J, Polasky, Daniel A, Yu, Fengchao, Nesvizhskii, Alexey I
Published in Nature communications (12.07.2023)
Published in Nature communications (12.07.2023)
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Journal Article
Unraveling the glycosylated immunopeptidome with HLA-Glyco
Bedran, Georges, Polasky, Daniel A, Hsiao, Yi, Yu, Fengchao, da Veiga Leprevost, Felipe, Alfaro, Javier A, Cieslik, Marcin, Nesvizhskii, Alexey I
Published in Nature communications (12.06.2023)
Published in Nature communications (12.06.2023)
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Journal Article
Fixed-Charge Trimethyl Pyrilium Modification for Enabling Enhanced Top-Down Mass Spectrometry Sequencing of Intact Protein Complexes
Polasky, Daniel A, Lermyte, Frederik, Nshanian, Michael, Sobott, Frank, Andrews, Phillip C, Loo, Joseph A, Ruotolo, Brandon T
Published in Analytical chemistry (Washington) (20.02.2018)
Published in Analytical chemistry (Washington) (20.02.2018)
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Journal Article
Collision induced unfolding of isolated proteins in the gas phase: past, present, and future
Dixit, Sugyan M, Polasky, Daniel A, Ruotolo, Brandon T
Published in Current opinion in chemical biology (01.02.2018)
Published in Current opinion in chemical biology (01.02.2018)
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Journal Article
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco
Polasky, Daniel A, Yu, Fengchao, Teo, Guo Ci, Nesvizhskii, Alexey I
Published in Nature methods (01.11.2020)
Published in Nature methods (01.11.2020)
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Journal Article
Recent advances in computational algorithms and software for large-scale glycoproteomics
Polasky, Daniel A., Nesvizhskii, Alexey I.
Published in Current opinion in chemical biology (01.02.2023)
Published in Current opinion in chemical biology (01.02.2023)
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Journal Article
CIUSuite 2: Next-Generation Software for the Analysis of Gas-Phase Protein Unfolding Data
Polasky, Daniel A, Dixit, Sugyan M, Fantin, Sarah M, Ruotolo, Brandon T
Published in Analytical chemistry (Washington) (19.02.2019)
Published in Analytical chemistry (Washington) (19.02.2019)
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Journal Article
Multiattribute Glycan Identification and FDR Control for Glycoproteomics
Polasky, Daniel A., Geiszler, Daniel J., Yu, Fengchao, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.03.2022)
Published in Molecular & cellular proteomics (01.03.2022)
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Journal Article
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics
Polasky, Daniel A., Geiszler, Daniel J., Yu, Fengchao, Li, Kai, Teo, Guo Ci, Nesvizhskii, Alexey I.
Published in Molecular & cellular proteomics (01.05.2023)
Published in Molecular & cellular proteomics (01.05.2023)
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Journal Article
Variable-Velocity Traveling-Wave Ion Mobility Separation Enhancing Peak Capacity for Data-Independent Acquisition Proteomics
Haynes, Sarah E, Polasky, Daniel A, Dixit, Sugyan M, Majmudar, Jaimeen D, Neeson, Kieran, Ruotolo, Brandon T, Martin, Brent R
Published in Analytical chemistry (Washington) (06.06.2017)
Published in Analytical chemistry (Washington) (06.06.2017)
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Journal Article
Ion Mobility-Mass Spectrometry Coupled to Droplet Microfluidics for Rapid Protein Structure Analysis and Drug Discovery
D’Amico, Cara I., Polasky, Daniel A., Steyer, Daniel J., Ruotolo, Brandon T., Kennedy, Robert T.
Published in Analytical chemistry (Washington) (27.09.2022)
Published in Analytical chemistry (Washington) (27.09.2022)
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Journal Article
A Modified Drift Tube Ion Mobility-Mass Spectrometer for Charge-Multiplexed Collision-Induced Unfolding
Vallejo, Daniel D, Polasky, Daniel A, Kurulugama, Ruwan T, Eschweiler, Joseph D, Fjeldsted, John C, Ruotolo, Brandon T
Published in Analytical chemistry (Washington) (02.07.2019)
Published in Analytical chemistry (Washington) (02.07.2019)
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Journal Article
Efficient Analysis of Proteome-Wide FPOP Data by FragPipe
Rojas Ramírez, Carolina, Espino, Jessica A., Jones, Lisa M., Polasky, Daniel A., Nesvizhskii, Alexey I.
Published in Analytical chemistry (Washington) (07.11.2023)
Published in Analytical chemistry (Washington) (07.11.2023)
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Journal Article
Quantitative proteome-wide O-glycoproteomics analysis with FragPipe
Polasky, Daniel A, Lu, Lei, Yu, Fengchao, Li, Kai, Shortreed, Michael R, Smith, Lloyd M, Nesvizhskii, Alexey I
Published in Analytical and bioanalytical chemistry (15.06.2024)
Published in Analytical and bioanalytical chemistry (15.06.2024)
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Journal Article
Collision Induced Unfolding Classifies Ligands Bound to the Integral Membrane Translocator Protein
Fantin, Sarah M, Parson, Kristine F, Niu, Shuai, Liu, Jian, Polasky, Daniel A, Dixit, Sugyan M, Ferguson-Miller, Shelagh M, Ruotolo, Brandon T
Published in Analytical chemistry (Washington) (17.12.2019)
Published in Analytical chemistry (Washington) (17.12.2019)
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Journal Article
Collision-Induced Unfolding Reveals Stability Differences in Infliximab Therapeutics under Native and Heat Stress Conditions
Vallejo, Daniel D, Kang, Jukyung, Coghlan, Jill, Ramírez, Carolina Rojas, Polasky, Daniel A, Kurulugama, Ruwan T, Fjeldsted, John C, Schwendeman, Anna A, Ruotolo, Brandon T
Published in Analytical chemistry (Washington) (07.12.2021)
Published in Analytical chemistry (Washington) (07.12.2021)
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Journal Article
Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data
Polasky, Daniel A, Dixit, Sugyan M, Keating, Michael F, Gadkari, Varun V, Andrews, Philip C, Ruotolo, Brandon T
Published in Journal of the American Chemical Society (08.04.2020)
Published in Journal of the American Chemical Society (08.04.2020)
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Journal Article
Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics
Burton, Nikolas R., Polasky, Daniel A., Shikwana, Flowreen, Ofori, Samuel, Yan, Tianyang, Geiszler, Daniel J., Veiga Leprevost, Felipe da, Nesvizhskii, Alexey I., Backus, Keriann M.
Published in Journal of the American Chemical Society (04.10.2023)
Published in Journal of the American Chemical Society (04.10.2023)
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Journal Article