Mass spectrometry-based chemical proteomics for drug target discoveries

II Fedorov, VI Lineva, IA Tarasova, MV Gorshkov - Biochemistry (Moscow), 2022 - Springer
Chemical proteomics, emerging rapidly in recent years, has become a main approach to
identifying interactions between the small molecules and proteins in the cells on a proteome …

Pyteomics 4.0: five years of development of a python proteomics framework

LI Levitsky, JA Klein, MV Ivanov… - Journal of proteome …, 2018 - ACS Publications
Many of the novel ideas that drive today's proteomic technologies are focused essentially on
experimental or data-processing workflows. The latter are implemented and published in a …

Ultrafast Proteomics

II Fedorov, SA Protasov, IA Tarasova… - Biochemistry (Moscow …, 2024 - Springer
Current stage of proteomic research in the field of biology, medicine, development of new
drugs, population screening, or personalized approaches to therapy dictates the need to …

DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry

MV Ivanov, JA Bubis, V Gorshkov, IA Tarasova… - Analytical …, 2022 - ACS Publications
Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on
minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method …

Boosting MS1-only proteomics with machine learning allows 2000 protein identifications in single-shot human proteome analysis using 5 min HPLC gradient

MV Ivanov, JA Bubis, V Gorshkov… - Journal of proteome …, 2021 - ACS Publications
Proteome-wide analyses rely on tandem mass spectrometry and the extensive separation of
proteolytic mixtures. This imposes considerable instrumental time consumption, which is one …

DirectMS1: MS/MS-free identification of 1000 proteins of cellular proteomes in 5 minutes

MV Ivanov, JA Bubis, V Gorshkov, IA Tarasova… - Analytical …, 2020 - ACS Publications
Proteome characterization relies heavily on tandem mass spectrometry (MS/MS) and is thus
associated with instrumentation complexity, lengthy analysis time, and limited duty cycle. It …

Deep learning powers protein identification from precursor ms information

Y Dai, Y Yang, E Wu, C Shen… - Journal of Proteome …, 2024 - ACS Publications
Proteome analysis currently heavily relies on tandem mass spectrometry (MS/MS), which
does not fully utilize MS1 features, as many precursors remain unselected for MS/MS …

Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples

MV Ivanov, AS Kopeykina… - Journal of the American …, 2024 - ACS Publications
Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a
method of choice for quantitative proteomic applications requiring high throughput analysis …

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

DA Abdrakhimov, JA Bubis, V Gorshkov… - Rapid …, 2021 - Wiley Online Library
RATIONALE One of the important steps in initial data processing of peptide mass spectra is
the detection of peptide features in full‐range mass spectra. Ion mobility offers advantages …

On the feasibility of using an ultra-fast DirectMS1 method of proteome-wide analysis for searching drug targets in chemical proteomics

EM Solovyeva, JA Bubis, IA Tarasova, AA Lobas… - Biochemistry …, 2022 - Springer
Protein quantitation in tissue cells or physiological fluids based on liquid
chromatography/mass spectrometry is one of the key sources of information on the …