Advanced Proteomics Techniques and Applications

DeepDetect: deep learning of peptide detectability enhanced by peptide digestibility

DeepDetect predicts peptide detectability using digestibility features, achieving higher accuracy than existing methods across multiple proteases.

A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation

The paper introduces an ion mobility-integrated gas phase fractionation (IM-GPF) method for rapid diaPASEF library generation, outperforming direct deconvolution and approaching offline fractionation performance.

Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection

The paper re-mines serum proteomics data to identify post-translational modifications associated with Zika and dengue infections, highlighting specific modifications linked to each virus.

Multi-Omics Data of Perturbation Studies are Determined by Memory Effects from Subculture

The paper shows that subculture memory effects increase variation in omics data from perturbation studies, improving deconvolution and revealing causal networks.

Multi cell line analysis of lysosomal proteomes reveals unique features and novel lysosomal proteins

The paper analyzes lysosomal proteomes across six cell lines to identify cell-type specific differences and novel lysosomal proteins.

Improved in situ Characterization of Proteome-wide Protein Complex Dynamics with Thermal Proximity Co-Aggregation

The paper introduces Slim-TPCA, an optimized method for proteome-wide characterization of protein complex dynamics, showing improved throughput and accuracy in identifying complex dissociation and association under glucose deprivation.

Proteome coverage after simultaneous proteo-metabolome liquid-liquid extraction

This study compares proteome coverage and extraction efficiency of different solubilization agents in proteo-metabolome analysis using SPM-LLE and direct cell lysis.

A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

This paper creates a mass spectrometry-based atlas of ECM proteins across 25 mouse organs, revealing shared and tissue-specific ECM protein profiles.

Super-resolution mass spectrometry enables rapid, accurate, and highly-multiplexed proteomics at the MS2-level

The paper demonstrates that super-resolution mass spectrometry with least-squares fitting enables highly-multiplexed, accurate, and precise shotgun proteomics at the MS2 level.

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.

Strategies for increasing the depth and throughput of protein analysis by plexDIA

This paper introduces plexDIA, a framework for increasing proteomics throughput and depth through multiplexed DIA, enabling more accurate protein quantification and single-cell analysis.

IDENTIFICATION AND QUANTIFICATION OF MATRISOME PROTEINS OF MOUSE KIDNEYS

This study identifies and quantifies matrisome proteins in healthy mouse kidneys using two extraction methods, finding 113 proteins including 22 new to the Matrisome Database.

midiaPASEF maximizes information content in data-independent acquisition proteomics

The paper introduces midiaPASEF, a DIA scan mode that enhances information content in proteomics, enabling precise precursor m/z determination and efficient automated processing.

HLAProphet: Personalized allele-level quantification of the HLA proteins

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.

Cleavable crosslinkers redefined by novel MS3-trigger algorithm

The paper introduces an MS3-trigger algorithm that improves the sensitivity and specificity of MS3-based crosslinker identification in crosslinking mass spectrometry.

Scribe: next-generation library searching for DDA experiments

Scribe improves library searching for DDA experiments by predicting fragmentation and retention times for all peptides, outperforming traditional database searching in sensitivity and precision.

MS1Connect: a mass spectrometry run similarity measure

MS1Connect measures similarity between mass spectrometry runs using MS1 scans, outperforming baselines in species prediction and correlating with MS2 scan similarities.

Semi-supervised machine learning for sensitive open modification spectral library searching

This paper integrates semi-supervised machine learning into the ANN-SoLo tool to improve spectral library searching for open modification peptides, increasing identification rates.

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.

High sensitivity proteome-scale search for crosslinked peptides using CRIMP 2.0

The paper introduces an upgraded CRIMP tool for detecting crosslinked peptides in XL-MS data, showing improved sensitivity and resolution of protein interactions.

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

This study develops multienzyme deep learning models for de novo peptide sequencing from mass spectrometry data, showing improved generalizability and sequence coverage across diverse protease digests and species.

Quality control for the target decoy approach for peptide identification

The paper introduces TargetDecoy, a Bioconductor package to assess and control the quality of the target-decoy approach for peptide identification in proteomics.

Efficient indexing of peptides for database search using Tide

The paper improves the peptide indexing component of the Tide search engine, reducing resource usage and enabling larger databases, while exploring the impact of digestion parameters and PTMs on statistical power.

A Multiplexed SEC-MS Approach to Systematically Study the Interplay Between Protein Assembly-States and Phosphorylation Events

The paper introduces SEC-MX, a method to simultaneously study protein assembly-states and phosphorylation events, and demonstrates its application in HEK293 and HCT116 cells.

A global atlas of substrate specificities for the human serine/threonine kinome

Positional scanning peptide arrays profile substrate sequence specificities across 303 human serine/threonine kinases, enabling computational kinase-substrate annotation and signaling pathway inference across the human phosphoproteome.

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

DPHL v2 improves upon DPHL v1 by including semi-tryptic peptides and protein isoforms, increasing identified and dysregulated proteins in colorectal cancer analysis.

Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo

The paper develops ultrasensitive proteome technologies for single-cell and low-input mouse embryos, enabling high-depth protein identification with minimal starting material.

Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing

This paper introduces Spectralis, a deep learning method for de novo peptide sequencing that improves sensitivity and precision in tandem mass spectrometry.

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

The paper summarizes recent developments in the Crux toolkit for analyzing bottom-up proteomics data, including speedups, new features, and tools.

promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling

promor provides an R package for analyzing label-free proteomics data and building predictive models using machine learning.