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MetabolomicsHigh-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry (Data-independent acquisition)

Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their ...

2023-10-26 | MTBLS2959 | MetaboLights
MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
MetabolomicsHigh-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry (Mixed-mode column chromatography)

Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their ...

2023-10-26 | MTBLS2497 | MetaboLights
ProteomicsSpecter - Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
These data cover all of the analyses described in the paper "Specter: linear deconvolution as a new paradigm for targeted analysis of data-independent acquisition mass spectrometry proteomics". Specifically, the data consist of - 20 DIA and DDA files from the HEK293T/synthetic phosphopeptides spike-...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2018-03-19 | PXD006722 | Pride
Proteomics Data-independent acquisition 
ProteomicsiDIA-QC: AI-empowered Data-Independent Acquisition Mass Spectrometry-based Quality Control
Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collected 2638 files acquired by data independent acquisition (DIA) and paired DDA files from mouse liver digests using 21 mass spectrometers acr...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-06 | PXD051878 | Pride
Quality control  data independent acquisition  machine learning 
ProteomicsIn-depth protein profiling of mouse hippocampal postsynaptic density using data-independent acquisition proteomics
In the present study, we catalogued the proteome of postsynaptic density (PSD) derived from the hippocampus of three-week old (P19) mice. samples in 100 min gradient time.
ORGANISM(S): Mus musculus (Mouse) 
2014-09-25 | PXD000590 | Pride
Brain Postsynaptic density Hippocampus Data-independent acquisition 
ProteomicsData-Independent Acquisition Enhancement of a Competitive Activity-Based Protein Profiling Platform for Kinase Inhibitor Screening
Kinase inhibitors represent a vital class of therapeutic agents widely used in cancer research, immunology, and other disease areas. Mass spectrometry (MS) employing specially designed small molecule kinase-binding probes has become an essential strategy for identifying novel kinase drug targets. Wh...
ORGANISM(S): Homo sapiens (Human) 
2026-02-23 | PXD072729 | Pride
Proteomics Mass spectrometry Activity-based protein profiling Kinase Data-independent acquisition 
ProteomicsData independent acquisition cross-linking/mass spectrometry
Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independe...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) Gallus gallus (Chicken) Equus caballus (Horse) 
2019-01-25 | PXD011036 | Pride
Xi Reproducibility Spectronaut Data independent acquisition Label-free Mass spectrometry Quantitation Cross-linking 
ProteomicsData Dependent-Independent Acquisition (DDIA) Proteomics
data for DDIA (Data Dependent-Independent Acquisition) experiment
ORGANISM(S): Homo Sapiens (human) 
2020-05-04 | MSV000085371 | MassIVE
ProteomicsLabel-free quantification in ion-mobility enhanced data-independent acquisition proteomics
Data-dependent acquisition (DDA) methods are a well-established tool for proteome analysis and have greatly expedited the field of shotgun proteomics. However, their serial and stochastic nature restricts their reproducibility and limits the detectable dynamic range to the peptides that ionize best....
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse) (Baker's yeast) Escherichia coli 
2016-03-29 | PXD002393 | Pride
Proteomics Mass spectrometry Label-free quantification Ion mobility separation Data-independent acquisition 
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