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MetabolomicsA Prototypic Small Molecule Database for Bronchoalveolar Lavage-Based Metabolomics
The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we descri...
2018-02-09 | MTBLS591 | MetaboLights
MetabolomicsMetabolic Database of Sepsis
SepsisLiMetDB is a curated metabolomics database characterizing sepsis-induced liver injury, comprising 2,894 metabolites identified from 88 longitudinal clinical samples (20 healthy controls, 36 sepsis without liver injury, 32 sepsis with liver injury) across four disease progression timepoints (D1...
2026-08-03 | MTBLS14459 | MetaboLights
MetabolomicsImproving Metabolite Identification with DecoID for Database-Assisted Deconvolution of Metabolomic MS/MS Spectra

Chimeric MS/MS spectra contain fragments from multiple precursor ions and therefore hinder compound identification in metabolomics. Historically, deconvolution of these chimeric spectra has been challenging and relied upon specific experimental methods that introduce variation in the ratios of pr...

2021-04-29 | MTBLS2207 | MetaboLights
ProteomicsSipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics
Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased dis...
ORGANISM(S): Escherichia coli 
2018-02-09 | PXD007587 | Pride
Machine learning Metaproteomics Database searching 
ProteomicsOpen database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching
Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation data of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag be hide. This is especially ...
ORGANISM(S): Campylobacter fetus subsp. fetus Burkholderia cenocepacia J2315 Burkholderia pseudomallei (strain K96243) Acinetobacter baumannii 
2020-06-24 | PXD018587 | Pride
Wide tolerant database searching Bacterial glycosylation Open searching Glycosylation Glycopeptides Post-translational modifications Proteomics Atypical glycosylation 
ProteomicsSimulated spectral library searching on TripleTOF phosphopeptide datasets
Synthetic phosphopeptides and enriched K562 cell phosphopeptides were analyzed using a TripleTOF 6600 mass spectrometer before and after enzymatic dephosphorylation. Dephosphorylated peptides identified by X!Tandem database searching were subjected to spectral simulation of all possible single phosp...
ORGANISM(S): Homo Sapiens (human) 
2019-12-03 | PXD012433 | JPOST Repository
ProteomicsIsobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)
A vast assortment of human cell lines is available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, we determined the relative protein abundance profiles of a panel of eight diverse, but comm...
ORGANISM(S): Homo sapiens (Human) 
2020-10-19 | PXD020806 | Pride
Faims Tmtpro Eclipse Sps-ms3 Multi-notch Rts 
UnknownSupplementary search methods versus bibliographic database searching to identify studies and study reports.
Not available
S-EPMC12606714 | biostudies-literature
UnknownDatabase searching by flexible protein structure alignment.
Not available
S-EPMC2279924 | biostudies-literature
ProteomicsFull-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics.
Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude of workflows have been developed for multiplexed analyses, the most quantitatively accurate method (SPS-MS3) suffers from long acquisition duty cycles. We built a new, real-time database search (...
ORGANISM(S): Homo sapiens (Human) 
2020-04-09 | PXD017823 | Pride
Multiplexed Orbiter Real-time search 
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