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MetabolomicsLiquid Chromatography-Mass Spectrometry Quantification of Phytochemicals in Withania somnifera Using Data-Dependent Acquisition, Multiple-Reaction-Monitoring, and Parallel-Reaction-Monitoring with an Inclusion List

Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of sev...

2024-07-10 | MTBLS10418 | MetaboLights
Proteomics29RNP kinase idetification - Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice)
The 29-kDa RNA protein (29RNP), which was originally identified in rice etioplasts, has increased phosphorylation levels during de-etiolation. Here, using heparin-sepharose enriched fractions, we identified a chloroplast kinase that phosphorylated 29RNP. The chloroplast kinase phosphorylated the 29R...
ORGANISM(S): Oryza sativa (Rice) 
2015-04-27 | PXD000951 | Pride
29rnp Kinase M/z list inclusion method 
MetabolomicsImproving the Screening Analysis of Pesticide Metabolites in Human Biomonitoring by Combining High-Throughput In Vitro Incubation and Automated LC-HRMS Data Processing
There is a current need to monitor human exposure to a large number of pesticides and other chemicals of emerging concern (CECs). This requires screening analysis with high confidence for these compounds and their metabolites in complex matrices, which is hampered by the fact that no reference stand...
2022-01-17 | MTBLS2402 | MetaboLights
MetabolomicsLipidCreator workbench to probe the lipidomic landscape - Platelet isolation and stimulation - DIA lipid mediator validation

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 | MTBLS1382 | MetaboLights
ProteomicsPicky - a simple online method designer for targeted proteomics
Picky is an online method designer for targeted proteomics. To assess the performance of PRM methods designed by Picky we carried out a benchmark experiment. As reference samples we used different amounts of human proteins spiked into 1.4 µg yeast lysate. These sample where analyzed in PRM and DDA m...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2017-08-04 | PXD007039 | Pride
Prm Benchmark Dda 
ProteomicsPRM analysis of phosphopeptides of Nab2, Foxk1, HURP, ERK1/2, NPM, and Hspa4 from ΔB-Raf:ER cells.
ΔB-Raf:ER cells were treated with U0126 or 4-HT for 30 min in four biological replicates. Total proteins from cell lysates were digested with Typsin/Lys-C mix, and phosphopeptides were enriched by IMAC using Fe-NTA columns. After data-dependent LC-MS/MS analysis, phosphopeptides of Nab2, Foxk1, HURP...
ORGANISM(S): Mus Musculus (mouse) 
2022-03-03 | PXD028826 | JPOST Repository
ProteomicsSlx5/8 alleviates replication stress by promoting mitotic progression
MCM-10 vs. wild type yeast differential analysis using label-free relative quantification and directed mass spectometry using RIPPER. Loss of Mcm10 causes replication stress. We uncovered that S. cerevisiae mcm10-1 mutants rely on the SUMO-targeted E3 ubiquitin ligase complex Slx5/8 and SUMO network...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2016-04-05 | PXD002607 | Pride
Yeast Directed mass spectrometry Lc-ms/ms 
MetabolomicsBridging Targeted (Zeno MRM-HR) and Untargeted (SWATH) LC–HRMS in a Single Run for Sensitive Exposomics

Traditionally, chemical exposure has been assessed by low-resolution mass spectrometry via targeted approaches due to the typically extremely low concentration of such compounds in biological samples. Nevertheless, untargeted approaches are now becoming a promising tool for a broader investigatio...

2025-08-28 | MTBLS10565 | 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
ProteomicsDiversity matters: Optimal collision energies for tandem mass spectrometric analysis of a large set of N-glycopeptides
Detailed energy dependence investigations were carried out on AGP digest using 2.2 pmol glycoprotein per run and on the mixture of AGP, fetuin and transferrin digests injecting 2.2 pmol from all glycoproteins in each run. Stepped CE settings were applied with 80% of the time allocated to the higher ...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Homo Sapiens (ncbitaxon:9606) 
2022-06-15 | MSV000089657 | MassIVE
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