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ProteomicsThe GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform
Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high throughput experiments. Most importantly, it enables results dependent acquisition (RDA) where search results can be used to guide data acquisition during acquisition. Th...
ORGANISM(S): Homo sapiens (Human) 
2023-03-13 | PXD040716 | Pride
Paser Glycoproteomics Glycopaser Results dependent acquisition (rda) Real-time search 
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 
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
ProteomicsAutomated 16plex plasma proteomics with real-time search and ion mobility mass spectrometry enables large scale profiling in naked mole-rats and mice.
Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully Automated Multiplexed Proteome Profiling Platform (AutoMP3) using the Hamilton VantageTM liquid handling robot capable of preparing hundreds to t...
ORGANISM(S): Mus musculus (Mouse) Heterocephalus glaber 
2021-02-04 | PXD022891 | Pride
Mouse and naked-mole rat plasma 
ProteomicsReal-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping
Cross-linking mass spectrometry (XL-MS) is a universal tool of molecular and structural biology for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental adva...
ORGANISM(S): Escherichia coli 
2023-03-20 | PXD037652 | Pride
Rtls E coli Cross-linking Diagnostic peaks Xl-ms Phox 
ProteomicsSensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics
Targeting cancer-specific HLA-peptide complexes is a promising immunotherapy approach, with mutated neoantigens offering high value for their immunogenicity and cancer-specificity. Selecting immunogenic targets requires personalized prioritization of cancer-specific immunopeptides. Mass spectrometry...
ORGANISM(S): Homo sapiens (Human) 
2025-06-20 | PXD059824 | Pride
Immunopeptidomics Real-time searches Antigen discovery 
ProteomicsComparison of LC-MS/MS and real-time PCR assays for the efficient detection of potentially allergenic silkworm
The silkworm (Bombyx mori) has long been considered a source of food and medicine due to its high nutritional, medicinal, and economic value in East Asia. However, in some sensitive individuals, silkworm consumption can cause allergenic reactions such as vomiting, asthma, and anaphylaxis. Therefore,...
ORGANISM(S): Bombyx mori (Silk moth) 
2024-05-24 | PXD042494 | Pride
Real-time pcr Model cookies Alpha-amlyase Lipoprotein Bombyx mori Silkworm Lc-ms/ms 
ProteomicsAutonomous Dissociation-type Selection for Glycoproteomics using a Real-Time Library Search
Tandem mass spectrometry (MS/MS) is the gold standard for intact glycopeptide identification, enabling peptide sequence elucidation and site-specific localization of glycan compositions. Beam-type collisional activation is generally sufficient for N-glycopeptides, while electron-driven dissociation ...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2024-11-15 | PXD055054 | Pride
N-glycopeptides Glycoproteomics Intelligent data acquisition Tandem mass spectrometry Beam-type collisional dissociation O-glycopeptides Product-dependent triggering Real-time library search Electron transfer dissociation 
ProteomicsMealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Proteomics
Mass spectrometry-based proteomics technologies are the prime methods for the high-throughput identification of proteins expressed in complex biological samples. Nevertheless, mass spectrometry’s technical limitations still hinder its ability to identify low abundance proteins in complex samples. Ch...
ORGANISM(S): Homo sapiens (Human) 
2020-10-27 | PXD017673 | Pride
Human Cell line Hek293 Lc-ms/ms 
ProteomicsSensitive and accurate proteome profiling of embryogenesis using Real-Time Search and TMTproC quantification
Multiplexed proteomics has become a powerful tool for investigating biological systems. Using balancer-peptide conjugates (e.g., TMTproC complementary ions) in the MS2 spectra for quantification circumvents the ratio distortion problem inherent in multiplexed proteomics. However, TMTproC quantificat...
ORGANISM(S): Ciona intestinalis x Ciona robusta Drosophila melanogaster (Fruit fly) Xenopus laevis (African clawed frog) 
2025-01-17 | PXD055647 | Pride
Ciona Tmtpro Xenopus Drosophila Multiplexing Ascend 
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