Lev I. Levitsky

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

The paper reanalyzes proteomic datasets to identify ADAR-mediated RNA editing events and finds 18 core recoded protein sites across human tissues.

IQMMA: an efficient MS1 intensity extraction using multiple feature detection algorithms for DDA proteomics

IQMMA improves protein quantitation in DDA proteomics by integrating multiple feature detection algorithms to extract more accurate MS1 intensities.

Unified and standardized mass spectrometry data processing in Python using spectrum_utils

The paper updates the spectrum_utils Python package to integrate mass spectrometry standards, enhance data processing, and unify visualization across proteomics and metabolomics applications.

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

This study compares DirectMS1Quant, an MS1-only quantitation method, with MS/MS-based methods like LFQ, TMT, and DIA, showing comparable efficiency despite shorter runtime.

A comprehensive evaluation of consensus spectrum generation methods in proteomics

The paper evaluates consensus spectrum generation methods in proteomics, finding BEST and BIN to be the most reliable for peptide identification.

Validating amino acid variants in proteogenomics using sequence coverage by multiple reads

The paper validates amino acid variants in proteogenomics by using multiple reads from overlapping peptides to improve variant reliability.

A proteomics sample metadata representation for multiomics integration, and big data analysis.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

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

AA_stat improves interpretation of open search results in proteomics by adding features for mass shift localization, modification inference, and calibration.

Proteome-Wide Analysis of ADAR-mediated Messenger RNA Editing During Fruit Fly Ontogeny

The paper identifies ADAR-mediated RNA editing sites in Drosophila proteomes across developmental stages and shows editing is phase-specific and enriched in synaptic and actomyosin functions.