The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms ( https://quant,ms.org/ ), an open-source cloud-based pipeline for massively parallel proteomics data analysis. We used quantms to reanalyze 83 public ProteomeXchange datasets, comprising 29,354 instrument files from 13,132 human samples, to quantify 16,599 proteins based on 1.03 million unique peptides. quantms is based on standard file formats improving the reproducibility, submission and dissemination of the data to ProteomeXchange.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399091 | PMC |
| http://dx.doi.org/10.1038/s41592-024-02343-1 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A proteogenomic analysis of the adiposity colorectal cancer relationship identifies GREM1 as a probable mediator.
Int J Epidemiol
December 2024
International Agency for Research on Cancer (IARC/WHO), Nutrition and Metabolism Branch, Lyon, France.
Background: Adiposity is an established risk factor for colorectal cancer (CRC). The pathways underlying this relationship, and specifically the role of circulating proteins, are unclear.
Methods: Utilizing two-sample univariable Mendelian randomization (UVMR), multivariable Mendelian randomization (MVMR), and colocalization, based on summary data from large sex-combined and sex-specific genetic studies, we estimated the univariable associations between: (i) body mass index (BMI) and waist-hip ratio (WHR) and overall and site-specific (colon, proximal colon, distal colon, and rectal) CRC risk, (ii) BMI and WHR and circulating proteins, and (iii) adiposity-associated circulating proteins and CRC risk.
Identification of Proteoforms Related to Flower Petaloid Through Proteogenomic Strategy.
Proteomes
January 2025
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430026, China.
is an aquatic plant with a high ornamental value due to its flower. Despite the release of several versions of the lotus genome, its annotation remains inefficient, which makes it difficult to obtain a more comprehensive knowledge when -omic studies are applied to understand the different biological processes. Focusing on the petaloid of the lotus flower, we conducted a comparative proteomic analysis among five major floral organs.
View Article and Find Full Text PDFNovel Integration of Spatial and Single-Cell Omics Data Sets Enables Deeper Insights into IPF Pathogenesis.
Proteomes
January 2025
Research & Development, AbbVie Bioresearch Center, Worcester, MA 01605, USA.
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease characterized by repetitive alveolar injuries with excessive deposition of extracellular matrix (ECM) proteins. A crucial need in understanding IPF pathogenesis is identifying cell types associated with histopathological regions, particularly local fibrosis centers known as fibroblast foci. To address this, we integrated published spatial transcriptomics and single-cell RNA sequencing (scRNA-seq) transcriptomics and adopted the Query method and the Overlap method to determine cell type enrichments in histopathological regions.
View Article and Find Full Text PDFStudy on Interaction Between 5-(4 Methoxyphenyl)-1-Phenyl-1H-1,2,3-Triazole with High-Abundant Blood Proteins and Identification of Low-Abundant Proteins by Serum Proteomics.
J Sep Sci
January 2025
Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education, Hainan Normal University, Haikou, China.
A comprehensive strategy, including spectroscopic, molecular simulation, proteomics, and bioinformatics techniques, was employed to investigate a novel triazole, 5-(4-methoxyphenyl)-1-phenyl-1H-1,2,3-triazole, its interactions with high-abundance blood proteins, and identification of low-abundance proteins. The binding constants and thermodynamic parameters of the triazole to two high-abundance blood globular proteins, human serum albumin, and human immunoglobulin G (HIgG), were obtained by spectroscopic techniques and computational chemistry. The two-dimensional gel electrophoresis in combination with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was employed to isolate and identify differentially expressed low-abundance proteins in human blood serum samples following exposure to the triazole.
View Article and Find Full Text PDFMultimodal data integration to predict atrial fibrillation.
Eur Heart J Digit Health
January 2025
Cardiovascular Division, Department of Medicine, University of Minnesota Medical School, 401 East River Parkway, Minneapolis, MN, USA.
Aims: Many studies have utilized data sources such as clinical variables, polygenic risk scores, electrocardiogram (ECG), and plasma proteins to predict the risk of atrial fibrillation (AF). However, few studies have integrated all four sources from a single study to comprehensively assess AF prediction.
Methods And Results: We included 8374 (Visit 3, 1993-95) and 3730 (Visit 5, 2011-13) participants from the Atherosclerosis Risk in Communities Study to predict incident AF and prevalent (but covert) AF.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!