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MetabolomicsMachine Learning-Based Retention Time Prediction of Trimethylsilyl Derivatives of Metabolites
In gas chromatography-mass spectrometry-based untargeted metabolomics, metabolites are identified by comparing mass spectra and chromatographic retention time with reference databases or standard materials. In that sense, machine learning has been used to predict the retention time of metabolites la...
2022-05-26 | MTBLS2841 | MetaboLights
MetabolomicsA novel strategy for mining and identification of acylcarnitines using data-independent-acquisition (DIA) based retention time prediction modeling and pseudo-characteristic fragmentation ions matching
It is a challenging work to screen, identify, and quantify acylcarnitines in complex biological samples. A method, based on the retention time (RT) prediction and data-independent acquisition strategies, was proposed for the large-scale identification of acylcarnitines using liquid chromatography co...
2021-10-06 | MTBLS1932 | MetaboLights
MetabolomicsCombining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Spring wheat (Triticum aestivum L.) was grown in a free-air carbon dioxide (CO2) enrichment (FACE) field experiment. Grain and biomass yield and its components were determined at maturity and the grain metabolome was analysed by gas chromatography-mass spectrometry (GC-MS) for elevated and ambient C...
2012-09-21 | MTBLS21 | MetaboLights
ProteomicsRetention time calibration for RP-HPLC at pH 9
The change in pH of the mobile phase drastically changes the retention mechanism of peptides, rendering currently available retention time prediction models useless. The aim of this study is to create a dataset of peptide retention times under basic (pH 9) HPLC conditions, allowing for the creation ...
ORGANISM(S): Homo sapiens (Human) 
2026-02-13 | PXD064311 | Pride
Hela Basic ph Rp-hplc 
ProteomicsGlycopeptide Relative Retention Time Prediction
A re-analysis of published data-dependent acquisition glycoproteomics datasets to demonstrate relative retention time prediction on glycopeptide identification and disambiguation of adduct states.
ORGANISM(S): Homo sapiens (Human) 
2020-04-01 | PXD018208 | Pride
Glycoproteomics 
ProteomicsPROCAL: A set of 40 peptide standards for retention time indexing, column performance monitoring and collision energy calibration
We describe PROCAL (ProteomeTools Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation char...
ORGANISM(S): artificial sequences 
2017-09-07 | PXD006832 | Pride
Retention time kit Peptide standard Retention time calibration Proteometools Synthetic peptide 
ProteomicsAssessing the relationship between mass window width and retention time scheduling on protein coverage for data-independent acquisition
Due to the technical advances of mass spectrometers especially the high scanning speed and high MS/MS resolution, the data independent acquisition mass spectrometry (DIA-MS) began to be widely used, which enables high reproducibility in both proteomic identification and quantification. The current D...
ORGANISM(S): Homo sapiens (Human) 
2019-07-01 | PXD013477 | Pride
Scheduling Rtwindia Window size Oribtrap fusion lumos Dia-ms 
ProteomicsHigh precision iRT retention time prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation
Targeted analysis of DIA data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted rete...
ORGANISM(S): Homo sapiens (Human) 
2016-07-14 | PXD004188 | Pride
Dia Retention time prediction 
ProteomicsRetention time as an extra dimension for proteome-wide cross-link identification
Chemical crosslinking methods have not been successfully applied to protein-protein interaction discovery mainly due to the computation complexity (O (n2)) issue. In a previous report, we proposed a decision tree searching strategy which can reduce complexity by orders of magnitude. In this study, w...
ORGANISM(S): Bos taurus (Bovine) Escherichia coli 
2021-07-29 | PXD024253 | Pride
Xl-ms Chemical crosslinking Proteome-wide cross-link identification Retention time 
ProteomicsPASS00724 - Raw DIA files and libraries used in the manuscript "Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry"
Data independent acquisition files and corresponding library files used to demonstrate the value of a set of conserved, commonly occurring peptide sequences to align chromatographic retention time between spectral libraries and DIA files.
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2018-08-23 | MSV000082842 | MassIVE
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