Advanced Proteomics Techniques and Applications

MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data

MSModDetector identifies PTM patterns in individual ion mass spectrometry data by detecting mass shifts and using linear programming to infer modifications.

Proteogenomics analysis of human tissues using pangenomes

The paper reanalyzes human tissue proteomics data using pangenome references to identify novel peptides and variants, demonstrating the effectiveness of proteogenomics approaches with pangenome data.

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

The paper introduces a clinical metaproteomics workflow that enables analysis of host-microbe dynamics in disease by integrating mass spectrometry and bioinformatics tools.

Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics

The paper presents an automated workflow for proteome and phosphoproteome sample preparation, enabling high-throughput clinical proteomics analysis of metastatic melanoma patients' plasma.

π-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing

π-PrimeNovo is a non-autoregressive deep learning model for de novo peptide sequencing that achieves higher accuracy and 69x faster performance than existing methods.

MultiStageSearch: a multi-step proteogenomic workflow for taxonomic identification of viral proteome samples adressing database bias

MultiStageSearch improves viral strain identification by combining proteomic and genomic databases, outperforming existing methods without relying on NCBI taxonomy.

Methodology for isolation of serum, cerebrospinal fluid, and hippocampal neuron proteins from rat and their analysis using mass spectrometry-based shotgun proteomics

The paper presents a method for isolating serum, cerebrospinal fluid, and hippocampal neuron proteins from rats and analyzing them using mass spectrometry-based shotgun proteomics.

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

The paper trains a deep learning model to predict fragment ion intensities, improving immunopeptide identification rates using timsTOF instruments.

Optimizing Proteomics Data Differential Expression Analysis via High-Performing Rules and Ensemble Inference

The paper identifies optimal workflow combinations for proteomics differential expression analysis using frequent pattern mining and ensemble inference, improving accuracy across multiple quantification platforms.

Integrated Proteomics analysis of baseline protein expression in pig tissues

The paper reanalyzes public pig proteomics data to map baseline protein expression across 14 organs and compares it with human orthologs.

Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Activated Ion-Tandem Mass Tags (AI-TMT)

This paper introduces AI-TMT, a method enhancing single-cell proteomics sensitivity by improving reporter ion generation, resulting in higher signal and faster analysis.

Communicating mass spectrometry quality information in mzQC with Python, R, and Java

The paper presents open-source software libraries for processing mzQC data in Python, R, and Java, enabling QC analysis and integration in mass spectrometry workflows.

Longitudinal fluctuations in protein concentrations and higher-order structures in the plasma proteome of kidney failure patients subjected to a kidney transplant

This study tracks longitudinal changes in the plasma proteome and complexome of kidney failure patients before and after transplantation, revealing acute phase protein dynamics and macromolecular complex formation during inflammation.

Unraveling the proteome landscape of mouse hematopoietic stem and progenitor compartment with high sensitivity low-input proteomics

This study develops a low-input proteomics workflow to analyze rare hematopoietic stem and progenitor cells, identifying 7,000 proteins and a novel marker for long-term hematopoietic stem cells.

Systematic identification of structure-specific protein-protein interactions

This study systematically identifies structure-specific protein-protein interactions using LiP-MS, demonstrating its application to alpha-synuclein in Parkinson's disease.

A Workflow for Improved Analysis of Cross-linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline

This paper introduces a workflow for improved XL-MS data analysis using PASEF, integrating MeroX and Skyline for better identification of cross-linked products.

CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics

CLIPPER 2.0 is a computational tool for peptide-level annotation and analysis of positional proteomics data, demonstrating its use on GluC and MMP9 cleavage in HeLa lysates.

Re-investigating the correctness of decoy-based false discovery rate control in proteomics tandem mass spectrometry

The paper investigates FDR control in proteomics MS/MS database searches, finding no strong evidence of issues in open modification or narrow window approaches after accounting for chimeric spectra and candidate differences.

MassDash: A Web-based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization

MassDash provides a web-based tool for visualizing and validating DIA mass spectrometry data across multiple software tools.

Dynamics of single-cell protein covariation during epithelial-mesenchymal transition

The paper quantifies protein covariation in single human cells during EMT, revealing dynamic protein-protein correlations that reflect biological regulation masked by cluster-average dynamics.

Analysis of tandem mass spectrometry data with CONGA: Combining Open and Narrow searches with Group-wise Analysis

The paper introduces CONGA, a method that combines narrow and open modification searches to improve detection of post-translational modifications while maintaining statistical power.

High-throughput nano-flow proteomics using a dual-column electrospray source

The paper introduces a dual-column electrospray source for nano-flow proteomics to improve throughput while maintaining sensitivity in low-input samples.

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology

This paper introduces CLASP, a cross-link assisted spatial proteomics method, to map sub-organelle proteomes and membrane protein topology in human mitochondria.

Pushing the Isotopic Envelope: When carrier channels pollute their neighbors signals

The paper investigates how impurities in isobaric labeling reagents can cause contamination in single-cell proteomics, leading to inaccurate quantification when carrier channels are overused.

Inserting Pre-Analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics With Sample Multiplexing

The paper introduces GoDigViewer to optimize GoDig assays by implementing chromatographic priming runs, significantly improving peptide-level quantification success rates in targeted pathway proteomics.

TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics

TIMAHAC enables high-throughput simultaneous analysis of plant phosphoproteomics and N-glycoproteomics, identifying 1,954 N-glycopeptides and 11,255 phosphopeptides in Arabidopsis under ABA treatment.

Profiling the organ membrane proteome dysregulation in the context of liver disease

This study identifies dysregulated membrane proteins in liver disease using peptidisc-based proteomics in mice, highlighting lipid metabolism and xenobiotic processing pathways.

Cheap, Robust and Versatile Two-Dimensional Chromatography system for Proteomics of Nanogram Scale Samples

The paper describes a 2D chromatography system for proteomics that improves coverage and intensity with nanogram-scale samples, showing benefits for phosphoproteomics and pull-down experiments.

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

APIR aggregates database search algorithms for proteomics to increase peptide identification while controlling FDR, outperforming individual methods on standard and real data.

Reanalysis of Orbitrap Astral DIA data demonstrates the capabilities of MS/MS-free proteomics to reveal new biological insights in disease-related samples

This study reanalyzes Orbitrap Astral DIA data using DirectMS1 to show it detects additional proteins and reveals new biological insights in disease-related samples.