Advanced Proteomics Techniques and Applications

Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics

The paper optimizes automated phosphopeptide enrichment to improve phosphoproteome coverage and sensitivity in low-input samples using LC-MS/MS.

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics

The paper introduces an automated sample preparation workflow for laser microdissection guided proteomics, validated on human tonsil tissue with high cell type specificity.

Searching Post-translational Modifications in Cross-linking Mass Spectrometry Data

This study introduces SeaPIC, an XL-MS tool for identifying post-translational modifications in protein-protein interactions and structures, successfully detecting previously undiscovered PTMs.

The remarkable similarity in the serum proteome between type 2 diabetics and controls

This study finds the serum proteome is remarkably similar between type 2 diabetics and controls, with major differences being glycations of abundant proteins and associations between BMI and a ternary complex.

MetaDIA: A Novel Database Reduction Strategy for DIA Human Gut Metaproteomics

MetaDIA reduces the search space for DIA gut metaproteomics by prioritizing peptides based on species and functional abundance, achieving results consistent with traditional DDA-based methods.

A Fit for Purpose Approach to Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics

The paper evaluates the detection of amino acid substitutions in shotgun proteomics by creating a ground-truth library using mixed bacterial proteomes and identifies sources of bias in substitution identification.

AlphaPept, a modern and open framework for MS-based proteomics

AlphaPept is an open-source framework for efficient processing of large MS-based proteomics datasets, achieving significant speed improvements using Python and machine learning.

Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular lifestyle.

This paper introduces a new sample preparation method, SPEED, which improves proteomic analysis of Bacillus subtilis spores by identifying more proteins and enabling differentiation between spore and vegetative cell proteins.

Subcellular thermal profiling enables the deep functional exploration of the mitochondrial proteome

The paper introduces mito-TPP, a thermal proteome profiling workflow for studying mitochondrial protein interactions and proteoforms, detecting over 180 proteins with multiple proteoform groups.

Deep plasma proteomics with data-independent acquisition: A fastlane towards biomarkers identification.

This study introduces a method combining plasma prefractionation and DIA to improve proteome coverage and depth, enabling robust biomarker identification in a COVID-19 cohort.

Target-decoy false discovery rate estimation using Crema

Crema is an open-source Python tool that implements target-decoy competition methods for estimating false discovery rates in proteomics experiments.

Lysis buffer selection guidance for mass spectrometry-based global proteomics including studies on the intersection of signal transduction and metabolism

This study compares four lysis buffers for proteomics, finding SDS most reliable and advocating a dual-sample approach to maximize proteome coverage.

Multilevel proteomic profiling of colorectal adenocarcinoma cell differentiation to characterize an intestinal epithelial model

This study uses multi-omic profiling to analyze Caco-2 cell differentiation, showing similar protein and pathway changes in spontaneous and medium-induced differentiation, with butyrate accelerating differentiation and altering protein expression related to host-microbiome interactions.

The 15-min (Sub)Cellular Proteome

The paper introduces a fast proteomic method using CE-DIA MS to profile the subcellular proteome of single cells with high sensitivity and coverage.

CURTAIN - A Unique Web-based tool for exploration and sharing of MS-based proteomics data

CURTAIN and CURTAIN-PTM are web-based tools for exploring and sharing MS-based proteomics data, enabling non-experts to analyze and visualize results through interactive features and shareable links.

High-throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF

This study develops a method to analyze the human lung ECM proteome using photocleavable surfactant and diaPASEF, identifying nearly 400 unique matrisome proteins.

Deep learning-based proteomics enables accurate classification of bulk and single-cell samples

This paper introduces a deep learning model called Proformer for classifying bulk and single-cell proteomic samples, showing improved performance over existing methods.

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

This study uses mass spectrometry proteomics to identify protein altering variants and map pQTLs, confirming target specificity and identifying novel variants not accessible by affinity proteomics.

Peptidoform analysis of IP-MS data allows detection of differentially present bait proteoforms

The paper introduces a workflow for IP-MS data to detect differentially present bait proteoforms, offering insights into protein function through peptidoform analysis.

Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python

Autoprot provides a Python module for proteomics data analysis, integrating R algorithms and interactive visualization for MS-based experiments processed with MaxQuant.

Enhanced feature matching in single-cell proteomics characterizes response to IFN-gamma and reveals co-existence of different cell states

The paper introduces DIA-ME, a method for single-cell proteomics that improves sensitivity and data completeness, revealing co-existing cell states in response to IFN-gamma.

Detecting predicted cancer-testis antigens in proteomics datasets of healthy and tumoral samples

The paper analyzes proteomics data to identify cancer-testis antigens (CTAs) in healthy and tumor tissues, finding 22 significantly enriched, 42 tumor-exclusive, and 32 healthy-abundant CTAs.

NovoLign: metaproteomics by sequence alignment

NovoLign provides a de novo metaproteomics pipeline for rapid taxonomic profiling and reference database creation, offering an alternative to database-based spectral annotation.

Making Proteomics Accessible: RokaiXplorer for interactive analysis of phospho-proteomic data

RokaiXplorer provides an intuitive web tool for phospho-proteomic data analysis and visualization, offering multiple functionalities and interactive features for researchers without specialized training.

Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesised proteins

The paper develops a workflow to enrich newly synthesized proteins in microbial communities using BONCAT and click chemistry, demonstrating its application in tracing microbial activity.

PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors

PepPre improves peptide identification by detecting accurate and comprehensive precursor ions, leading to higher PSM and peptide identifications compared to existing methods.

Community-based peptidomic clustering reveals pathogen-specific proteolytic signatures in wounds

The paper develops a computational workflow to cluster peptides in peptidomic data, revealing pathogen-specific proteolytic signatures in wound fluids.

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification

DeepRescore2 improves phosphopeptide identification using deep learning, leading to more phosphosites detected and new biological insights in liver cancer.

Quality control of variant peptides identified through proteogenomics- catching the (un)usual suspects

This paper introduces PgxSAVy, a tool for quality control of variant peptides in proteogenomics, which improves accuracy in identifying true variants and annotates their disease relevance.

msqrob2PTM: differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level

The paper introduces msqrob2PTM, a workflow for differential abundance and usage analysis of PTMs and peptidoforms in proteomics data, showing it performs on par or better than existing methods.