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MetabolomicsPublic LC-Orbitrap-MS/MS Spectral Library for Metabolite Identification

Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics studies require high-quality spectral libraries for reliable metabolite identification. We have constructed EMBL-MCF (European Molecular Biology Laboratory-Metabolomics Core Facility), an open LC-MS/MS spectral library ...

2020-09-28 | MTBLS1861 | MetaboLights
MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
ProteomicsDirect data-independent acquisition proteomics with in silico spectral libraries by deep learning
Data-independent acquisition (DIA) proteomics allows systematic and unbiased measurement of protein samples and enables fast quantitative analysis of large cohorts of samples. However, sample-specific spectral libraries are usually required prior to perform DIA experiments. The libraries are built b...
ORGANISM(S): Homo Sapiens 
2019-12-02 | PXD014108 |
ProteomicsReproducibility, specificity and accuracy of DIA quantification - Spectral Libraries
For the complete description see the manuscript. Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analy...
ORGANISM(S): Mus musculus (Mouse) 
2019-11-08 | PXD012987 | Pride
Dia Label-free quantification Peptide identification Spectral library Data-independent acquisition 
ProteomicsProtein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics
Mass spectrometry-based proteomics is challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid, reducing the sensitivity, specificity and reproducibility of protein identifica...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2022-01-21 | MSV000088714 | MassIVE
ProteomicsExploration of Artificial Intelligence-Based Spectral Libraries for Data Independent Acquisition in Complex Ocean Metaproteomic Analyses
Ocean metaproteomics provides valuable insights into the structure and function of marine microbial communities. Yet, ocean samples are challenging due to their extensive biological diversity that results in a very large number of peptides with a large dynamic range. This study characterized the cap...
ORGANISM(S): environmental samples <bacteria Bacteria 
2025-09-29 | PXD057948 | Pride
Dda dia ocean metaproteomics proteomics 
ProteomicsImproved sensitivity of immunopeptidomics by leveraging available large-scale pan-HLA spectral libraries and data-independent acquisition
Mass spectrometry is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across HLA allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery-driven and data-dependent tandem mass spectrometry acquisition is commonly used, ...
ORGANISM(S): Homo sapiens (Human) 
2021-04-13 | PXD022950 | Pride
Pan-hla Immunopeptidomics Dia 
ProteomicsMSLibrarian: Optimized predicted spectral libraries for DIA proteomics
Data-independent mass spectrometry is the method of choice for deep, consistent and accurate single-shot profiling in bottom-up proteomics. While classic workflows required auxiliary DDA-MS analysis of subject samples to derive prior knowledge spectral libraries for targeted quantification from DIA-...
ORGANISM(S): Mus musculus (Mouse) Saccharomyces cerevisiae (Baker's yeast) 
2022-01-17 | PXD028901 | Pride
Q-exactive Predicted spectral library Dia Hf-x Lfq bench 
ProteomicsA primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics
Comprehensive spectral libraries are essential in sequential window acquisition of all theoretical mass spectra (SWATH-MS) based high throughput proteomic studies. Even though SWATH-MS assays provide robust quantitative proteomics data its applications to human T-cell studies are limited by the lack...
ORGANISM(S): Homo sapiens (Human) 
2020-10-19 | PXD019446 | Pride
Human Swath Spectral library Primary t-cells 
ProteomicsRat retinae data for use as spectral library, for pathway remodelling as well as protein mapping
Spectral libraries generated by data-dependent acquisition (DDA) are a useful tool for the analysis of data created by data-independent acquisition (DIA) in mass spectrometry. The quality of DIA analysis is dependent on the quality of the spectral library. We used retinal rat tissue to create a spec...
ORGANISM(S): Rattus norvegicus (Rat) 
2021-06-08 | PXD021937 | Pride
Lc-msms Rat Retina proteome Data-independent acquisition Spectral library 
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