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MetabolomicsStreamlining LC-MS/MS Data Analysis in R with Open-Source *xcms* and *RforMassSpectrometry*: An End-to-End Workflow

Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adapta...

2024-08-26 | MTBLS8735 | MetaboLights
MetabolomicsTroubleshooting in Large-Scale LC-ToF-MS Metabolomics Analysis: Solving Complex Issues in Big Cohorts
Metabolomics, understood as the science that manages the study of compounds from the metabolism, is an essential tool for deciphering metabolic changes in disease. The experiments rely on the use of high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-...
2019-12-12 | MTBLS1133 | MetaboLights
MetabolomicsOrgan-Resolved Untargeted LC-MS/MS Profiling of Putative Metabolite Families in Aerial Organs of Vitex negundo L

Background/Objectives: Vitex negundo L. is a multi-part medicinal and aromatic plant, but organ-resolved chemical information for its aerial organs remains incomplete. This study generated an exploratory paired untargeted liquid chromatography–tandem mass spectrometry (LC-MS/MS) dataset for flowe...

2026-09-13 | MTBLS15653 | MetaboLights
ProteomicsFast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DDA dataset)
We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine lear...
ORGANISM(S): Citrobacter Freundii (ncbitaxon:546) Streptococcus Agalactiae 2603v/r (ncbitaxon:208435) Staphylococcus Aureus Subsp. Aureus Nctc 8325 (ncbitaxon:93061) Streptococcus Mitis (ncbitaxon:28037) Klebsiella Oxytoca (ncbitaxon:571) Staphylococcus Epidermidis Atcc 12228 (ncbitaxon:176280) Enterococcus Faecalis V583 (ncbitaxon:226185) Enterobacter Aerogenes Kctc 2190 (ncbitaxon:1028307) Proteus Mirabilis (ncbitaxon:584) Escherichia Coli K-12 (ncbitaxon:83333) Enterobacter Cloacae (ncbitaxon:550) Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (ncbitaxon:272620) Pseudomonas Aeruginosa Pao1 (ncbitaxon:208964) Staphylococcus Saprophyticus Subsp. Saprophyticus Atcc 15305 (ncbitaxon:342451) Staphylococcus Haemolyticus Jcsc1435 (ncbitaxon:279808) 
2019-05-16 | MSV000083784 | MassIVE
ProteomicsFast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DIA dataset)
We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine lear...
ORGANISM(S): Citrobacter Freundii (ncbitaxon:546) Streptococcus Agalactiae 2603v/r (ncbitaxon:208435) Staphylococcus Aureus Subsp. Aureus Nctc 8325 (ncbitaxon:93061) Streptococcus Mitis (ncbitaxon:28037) Klebsiella Oxytoca (ncbitaxon:571) Staphylococcus Epidermidis Atcc 12228 (ncbitaxon:176280) Enterococcus Faecalis V583 (ncbitaxon:226185) Enterobacter Aerogenes Kctc 2190 (ncbitaxon:1028307) Proteus Mirabilis (ncbitaxon:584) Escherichia Coli K-12 (ncbitaxon:83333) Enterobacter Cloacae (ncbitaxon:550) Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (ncbitaxon:272620) Pseudomonas Aeruginosa Pao1 (ncbitaxon:208964) Staphylococcus Saprophyticus Subsp. Saprophyticus Atcc 15305 (ncbitaxon:342451) Staphylococcus Haemolyticus Jcsc1435 (ncbitaxon:279808) 
2019-05-16 | MSV000083793 | MassIVE
ProteomicsExtending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-based Quantitation in Proteomic LC/MS/MS
Two-dimensional separation by nano-LC and trapped ion mobility spectrometry (TIMS) prior to Q-TOF tandem mass spectrometry significantly improves the accuracy of isobaric tag-based quantitation in proteome analysis without the need for additional measurement time for TIMS insertion. The obtained pea...
ORGANISM(S): Cellular Organisms 
2020-05-22 | PXD018650 | JPOST Repository
MetabolomicsUHPLC-Q-TOF MS-Based Serum Metabolomics Reveals the Therapeutic Effects of Berberine and Wumei Wan on APCmin/+ Mice

APCmin/+ mice (8-week-old) and wild-type C57BL/6 controls were divided into MOD (saline), BBR (100 mg/kg berberine), WMW (17 g/kg Wu Mei Wan), and CON (saline) groups. All mice received daily gavage for 10 weeks under a 60% high-fat diet. Serum samples were collected after euthanasia and subjecte...

2025-10-16 | MTBLS12598 | MetaboLights
UnknownDiscovery of novel serum peptide biomarkers for cholangiocarcinoma recurrence through MALDI-TOF MS and LC-MS/MS peptidome analysis.
Not available
S-EPMC11746940 | biostudies-literature
UnknownMRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments.
Not available
S-EPMC3072341 | biostudies-literature
UnknownPeptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS.
Not available
S-EPMC8360550 | biostudies-literature
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