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IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics

Journal of proteome research, 2023-09, Vol.22 (9), p.2827-2835

2023

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Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO

Journal of fungi (Basel), 2023-03, Vol.9 (3), p.351

2023

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Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting

Proteomics (Weinheim), 2019-02, Vol.19 (3), p.e1800280-n/a

2019

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Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support

Rapid communications in mass spectrometry, 2021-01, p.e9045-e9045

2021

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HUMOS: How to Understand My Orbitrap Spectrum?An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics

Journal of proteome research, 2020-10, Vol.19 (10), p.3910-3918

2020

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Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

Journal of proteome research, 2021-04, Vol.20 (4), p.1864-1873

2021

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Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution

Environmental science. Nano, 2019-04, Vol.6 (4), p.1089-1098

2019

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PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety

Journal of the American Society for Mass Spectrometry, 2020-10, Vol.31 (10), p.2053-2060

2020

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DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry

Analytical chemistry (Washington), 2022-09, Vol.94 (38), p.13068-13075

2022

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DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes

Analytical chemistry (Washington), 2020-03, Vol.92 (6), p.4326-4333

2020

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On the utility of ultrafast MS1-only proteomics in drug target discovery studies based on thermal proteome profiling method

Analytical and bioanalytical chemistry, 2024-07, Vol.416 (18), p.4083-4089

2024

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Proteomics‐based scoring of cellular response to stimuli for improved characterization of signaling pathway activity

Proteomics (Weinheim), 2023-03, Vol.23 (5), p.e2200275-n/a

2023

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Comparative evaluation of label‐free quantification methods for shotgun proteomics

Rapid communications in mass spectrometry, 2017-04, Vol.31 (7), p.606-612

2017

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IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics

Journal of proteome research, 2018-07, Vol.17 (7), p.2249-2255

2018

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Improving the Protein Inference from Bottom-Up Proteomic Data Using Identifications from MS1 Spectra

Journal of the American Society for Mass Spectrometry, 2021-05, Vol.32 (5), p.1258-1262

2021

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AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results

Journal of proteomics, 2021-09, Vol.248, p.104350-104350, Article 104350

2021

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Validation of Peptide Identification Results in Proteomics Using Amino Acid Counting

Proteomics (Weinheim), 2018-12, Vol.18 (23), p.e1800117-n/a

2018

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A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

Journal of proteome research, 2022-06, Vol.21 (6), p.1566-1574

2022

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Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy

Applied microbiology and biotechnology, 2020-05, Vol.104 (9), p.4027-4041

2020

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Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing

Journal of proteome research, 2023-06, Vol.22 (6), p.1695-1711

2023

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Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues

Journal of proteomics, 2021-01, Vol.231, p.104022-104022, Article 104022

2021

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On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics

Biochemistry (Moscow), 2022-11, Vol.87 (11), p.1342-1353

2022

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Multi-Omics Analysis of Glioblastoma Cells’ Sensitivity to Oncolytic Viruses

Cancers, 2021-10, Vol.13 (21), p.5268

2021

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MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity

Journal of proteome research, 2017-11, Vol.16 (11), p.3989-3999

2017

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Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells

Oncotarget, 2018-01, Vol.9 (2), p.1785-1802

2018

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IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics

Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO

Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting

Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support

HUMOS: How to Understand My Orbitrap Spectrum?An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution

PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety

DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry

DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes

On the utility of ultrafast MS1-only proteomics in drug target discovery studies based on thermal proteome profiling method

Proteomics‐based scoring of cellular response to stimuli for improved characterization of signaling pathway activity

Comparative evaluation of label‐free quantification methods for shotgun proteomics

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics

Improving the Protein Inference from Bottom-Up Proteomic Data Using Identifications from MS1 Spectra

AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results

Validation of Peptide Identification Results in Proteomics Using Amino Acid Counting

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy

Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing

Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues

On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics

Multi-Omics Analysis of Glioblastoma Cells’ Sensitivity to Oncolytic Viruses

MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity

Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells

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