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MetabolomicsLipidCreator workbench to probe the lipidomic landscape - Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators, Agilent QTof

Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope...

2020-04-15 | MTBLS1334 | MetaboLights
MetabolomicsLipidCreator workbench to probe the lipidomic landscape - Collision Energy Optimization and Fragment Intensity Prediction for Lipid Mediators, Thermo QExactive HF

Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope...

2020-04-15 | MTBLS1333 | MetaboLights
MetabolomicsUntargeted metabolomics profiling reveals exercise intensity-dependent alterations in Thoroughbred racehorses’ plasma after routine conditioning sessions

Thoroughbred (TB) racehorses are subjected to rigorous conditioning programs involving exercise sessions of various types, distances and intensities. These programs aim to optimize both their physical and mental capabilities, which are essential to achieve maximal performance. Conventional invest...

2024-01-16 | MTBLS8285 | MetaboLights
MetabolomicsImprovement of prediction ability by integrating multi-omic datasets in barley

BACKGROUND: Genomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in plant breeding. However, using predictors that are biologically closer to the phenotypes such as transcriptome and metabolome may...

2022-03-18 | MTBLS1561 | MetaboLights
ProteomicsSpectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag Generation
Here's a suggested Project Description for your PRIDE submission: Project Description This dataset contains mass spectrometry raw files used as training data for SpecFormer, a transformer-based ion intensity prediction model integrated within PatternLab for Proteomics (Spectral Cruncher module). Th...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2026-02-16 | PXD069898 | Pride
Ion intensity prediction Multi-species omics Single-cell proteomics 
MetabolomicsPrediction and evaluation of the effect of pre-centrifugation sample management on the measurable untargeted LC-MS plasma metabolome

Optimal handling is the most important means to ensure adequate sample quality. We aimed to investigate whether pre-centrifugation delay time and temperature could be accurately predicted and to what extent variability induced by pre-centrifugation management can be adjusted for. We used untarget...

2021-10-13 | MTBLS2259 | MetaboLights
ProteomicsProsit: Proteome-wide prediction of peptide tandem mass spectra by deep learning
In this study, we extended the ProteomeTools peptide library (PROPEL, see PXD004732 and PXD010595) to train a deep neural network resulting in chromatographic retention time and fragment ion intensity predictions for (tryptic) peptides that exceed the quality of the experimental data.
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Caenorhabditis Elegans (ncbitaxon:6239) 
2021-03-12 | MSV000087047 | MassIVE
ProteomicsFragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF
Immunopeptidomics plays a crucial role in identifying targets for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-07-17 | MSV000092456 | MassIVE
ProteomicsIntensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links
Rescoring of protein-RNA cross-links using retention time and intensity prediction.
ORGANISM(S): Escherichia coli 
2025-11-24 | PXD048145 | Pride
Lc-msms Protein-rna cross-links Bottom-up proteaomics 
TranscriptomicsGenome-wide SNP signal intensity scanning to find genes differentiating cows with ovarian pathologies from healthy cows
Ovarian cysts and ovarian hypoplasia are common ovarian pathologies in cattle. The development of these pathologies can be attributed to factors such as uterine infection, stress, milk production, age, reproductive time and inherited genetics. The most common detection procedures are via rectal palp...
ORGANISM(S): Bos taurus 
2017-08-22 | E-MTAB-4874 | biostudies-arrayexpress
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