Advanced Proteomics Techniques and Applications

The paper introduces an advanced proteomics strategy using mass spectrometry to comprehensively profile ADP-ribosylation sites, identifying over 11,000 unique peptides and 7,000 sites in HeLa cells.

The paper introduces a method to improve spectral library coverage in DIA proteomics by using multiple characteristic intensity patterns, achieving near-complete coverage without increasing false discovery rates.

This study profiles lysine-acetylated proteins in normal human urine using immunoaffinity enrichment and mass spectrometry, identifying 629 acetylation sites on 315 proteins.

MaxQuant.Live enables real-time global targeting of over 25,000 peptides by combining shotgun and targeted proteomics approaches.

The paper introduces a method to automatically detect modifications in proteomics experiments from mass spectra and provides open-source implementations.

The paper creates a proteome and transcriptome atlas of 29 human tissues, revealing differences in mRNA-protein abundance and challenges in proteogenomics.

DIAlignR improves retention time alignment in SWATH-MS data by aligning raw MS2 chromatograms, outperforming existing methods and reducing alignment error significantly.

COPAL aligns complexome profiles to identify changes in mitochondrial protein complex abundance caused by Barth syndrome mutations.

The paper develops a computational tool to analyze protein complex behavior across human cell types using mass spectrometry data and provides a web service for co-regulation analysis.

The paper introduces a method to quantify protein complexes using SEC-SWATH-MS and identifies 462 complexes from HEK293 cells.

MoMo provides a method to assign statistical confidence to PTM motifs, showing improved accuracy over motif-x and offering a web server and software tool.

The paper evaluates a DIWA method to decompress isobaric labelling ratios by using narrow isolation widths for quantification and standard widths for identification, improving accuracy while maintaining coverage.

The paper introduces an averaging strategy to reduce variability in FDR estimates from target-decoy competition in shotgun proteomics.

This study evaluates the sub-cellular resolution of 29 spatial proteomics experiments using QSep to provide a quantitative assessment of their ability to resolve sub-cellular niches.

LFAQ improves label-free absolute protein quantification by correcting MS intensity biases using predicted peptide quantitative factors, achieving higher accuracy and precision, especially for low-abundance proteins.

Q4SRM is a software tool that rapidly assesses the quality of targeted proteomics experiments by monitoring stable-isotope labeled standards.

msCRUSH clusters tandem mass spectra using LSH, achieving faster speed and better sensitivity than existing tools, improving peptide identification.

This paper introduces a Bayesian mixture model for spatial proteomics to probabilistically assign proteins to sub-cellular locations and quantify uncertainty in classification.

The paper introduces Triqler, a probabilistic graphical model for shotgun proteomics that controls FDR and improves sensitivity in protein quantification.

The paper introduces PIA, a tool for protein inference in proteomics, highlights its support for PSI standards, and benchmarks it against a dataset for isoform detection.

RawTools extracts and analyzes data from Thermo Orbitrap raw files to aid in mass spectrometer system management and performance optimization.

The paper introduces iProteinDB, a database integrating Drosophila phosphoproteomics data with other PTM datasets to identify conserved phosphosites across species.

This study uses PCT-SWATH to analyze proteomic changes in HCC biopsy samples, identifying 23 upregulated pathways and 13 downregulated ones, with notable changes in virus-infection-related proteins in HBV+ patients.

The paper introduces a regression model called Siren to improve peptide detection in DIA mass spectra by accounting for isotope peak interference.

SCoPE-MS combines acoustic cell lysis with isobaric tandem-mass-tag carrier channels to quantify over a thousand proteins in single mammalian cells, resolving cancer cell types and stem cell differentiation.

ProteomeGenerator enables sample-specific proteome discovery by integrating transcriptome sequencing and high-accuracy mass spectrometry, identifying non-canonical protein isoforms and improving proteogenomic analysis.

The paper introduces Xi-MPA, a method for in-search assignment of monoisotopic peaks in cross-linking mass spectrometry, which improves peptide identification without compromising accuracy.

Open-pFind improves peptide identification in shotgun proteomics by handling complex modifications and increasing identification rates and speed.

The paper identifies seminal fluid proteins in Drosophila melanogaster using label-free quantitative proteomics, finding novel candidates and re-evaluating previously reported proteins.

The paper develops a model to accurately quantify proteoform stoichiometries using mass-spectrometry data without external standards.