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MetabolomicsPreterm birth is associated with xenobiotics and predicted by the vaginal metabolome
Spontaneous preterm birth (sPTB) is a leading cause of maternal and neonatal morbidity and mortality, yet its prevention and early risk stratification are limited. Previous investigations have suggested that vaginal microbes and metabolites may be implicated in sPTB. Here we performed untargeted met...
2022-11-21 | MTBLS702 | MetaboLights
MetabolomicsComputational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus
The aqueous extract of yerba mate, a South American tea beverage made from Ilex paraguariensis leaves, has demonstrated bactericidal and inhibitory activity against bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). The gas chromatography-mass spectrometry (GC-MS) ana...
2015-03-19 | MTBLS170 | MetaboLights
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 
ProteomicsDirect glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced association tandem mass spectrometry and predicted spectral library searching
Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a novel computationa...
ORGANISM(S): Homo sapiens (Human) 
2016-08-17 | PXD002803 | Pride
Glycopeptide Lc-msms 
ProteomicsSimulated phosphopeptide spectral library for confident site localization
We have developed a new workflow to unambiguously localize phosphorylation sites on proteins. We demonstrate that spectral matching of phosphopeptide datasets against a library of the well-simulated spectra provided higher sensitivity for confident site localization than other tested programs. To co...
ORGANISM(S): Homo sapiens (Human) 
2015-03-17 | PXD000474 | Pride
Synthetic peptide Simulated spectral library Hela Phosphopeptide Lc-ms/ms 
ProteomicsReal-time spectral library matching for sample multiplexed quantitative proteomics
Sample multiplexed quantitative proteomics has proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data ac...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932) 
2023-02-03 | MSV000091200 | MassIVE
ProteomicsA comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to e...
ORGANISM(S): Halobacterium salinarum 
2023-09-21 | PXD042770 | Pride
Dia Data-independent acquisition Swath Halobacterium salinarum nrc-1 Spectral assay library Dda Data-dependent acquisition 
ProteomicsEvaluation of library-free strategies for phosphoproteomics and ubiquitinomics data-independent acquisition data
Phosphoproteomics and ubiquitinomics data-independent acquisition MS data is generally analyzed using a DDA spectral library. Performance of different library-free strategies of analyzing phosphoproteomics and ubiquitinomics DIA MS data are not evaluated. In this study, we assess three library-free ...
ORGANISM(S): Homo Sapiens 
2023-05-17 | PXD037870 |
ProteomicsSpectral Libraries in proteomics
evaluated approaches for building a spectral library in plasma proteomics on a timsTOF HT system. Furthermore, the relationship between measurement time, library depth and number of protein and peptide identification for semi-high throughput plasma proteomics applications was assessed.
ORGANISM(S): Homo sapiens (Human) 
2025-11-17 | PXD058337 | Pride
Timstof ht Plasma proteomics Spectral library Data independent acquisition 
ProteomicsA Labrador DIA spectral assay library - resource for proteomics research in dogs
The domestic dog, Canis lupus familiaris, plays a vital role as companion or service animal, and the well-being and healthy aging of dogs is gaining importance. Proteins are key actors in cells, tissues and body fluids, and the ability to measure their composition and abundance is crucial to underst...
ORGANISM(S): Canis familiaris (Dog) (Canis lupus familiaris) 
2025-12-16 | PXD052902 | Pride
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