Alexey I. Nesvizhskii

MSFragger-Labile improves the analysis of labile post-translational modifications by incorporating modification-specific fragment ions into mass spectrometry searches.

HLAProphet improves HLA protein quantification by using personalized allele information from DNA sequencing, increasing peptide identifications and aligning with RNA expression and loss of heterozygosity.

The paper introduces MSFragger-DIA, a tool for fast and sensitive peptide identification from DIA proteomics data, integrated into FragPipe, and demonstrates its performance across various sample types.

MSBooster improves peptide identification rates by integrating deep learning-based features into existing workflows with MSFragger and Percolator.

The paper develops a method to automatically detect diagnostic spectral features for post-translational modifications in mass spectrometry data, improving PTM identification and localization rates.

The paper demonstrates improved proteomic depth using DIA-NN and FragPipe for dia-PASEF data, achieving higher sensitivity and quantification in complex samples.

The paper introduces a method to accurately identify glycan compositions in glycopeptide spectra and control false discovery rates, integrating it into a computational pipeline for glycoproteomics analysis.

This paper introduces LUX-MS, a light-triggered optoproteomic technology to map surfaceome receptor interactions and nanoscale organization, revealing insights into intercellular signaling and drug action.

IonQuant improves label-free proteomic quantification by implementing FDR-controlled match-between-runs, achieving faster speed and higher protein quantification than MaxQuant.

PTM-Shepherd automates analysis of post-translational modifications from open search proteomics data, improving detection of artifacts and biases across experiments.

MSFragger-Glyco improves glycopeptide identification in N- and O-glycoproteomics data, increasing glycoPSMs and revealing new glycan trends.

The paper introduces MSFragger and IonQuant for fast analysis of timsTOF PASEF data, showing improved peptide identification and quantification compared to existing tools.

This paper introduces a QconCAT-based proteomics method to measure allele-specific protein expression (ASPE) and identifies cis-regulatory variants affecting UGT2B15 in human livers.

DIA-Pipe enables automated identification and quantification of post-translational modification peptides from DIA data without a pre-existing spectral library.

The paper introduces the Omics Discovery Index, a platform to search and link public omics datasets across different fields, addressing challenges in data organization and accessibility.