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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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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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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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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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Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution† †Electronic supplementary information (ESI) available: Supporting Information 1: Experimental details; figures and tables; protein abundance and corresponding sigmoid fit for all of the differentially abundant proteins detected in pH and temperature perturbation experiments. Supporting Information 2: Complete list of quantified proteins in all LC–MS runs in

Environmental science. Nano, 2019-03, Vol.6 (4), p.1089-1098

2019

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Structure-dependent performance of single-walled carbon nanotube films in transparent and conductive applications

Carbon (New York), 2020-05, Vol.161, p.712-717

2020

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Recognition of amino acid enrichments in ultra tolerant search results facilitates PTM crosstalk discovery in large scale proteomics

The FASEB journal, 2021-05, Vol.35, p.n/a

2021

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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

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

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

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

Structure-dependent performance of single-walled carbon nanotube films in transparent and conductive applications

Recognition of amino acid enrichments in ultra tolerant search results facilitates PTM crosstalk discovery in large scale proteomics

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