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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 
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 
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 
ProteomicsTemporal proteomic profiling of SH-SY5Y differentiation with retinoic acid using a FAIMS and Real-Time Searching strategy
The SH-SY5Y cell line is often used as a surrogate for neurons in cell-based studies. This cell line is frequently differentiated with all-trans retinoic acid (ATRA) over a 7-day period which confers neuron-like properties to the cells. However, no analysis of proteome remodeling has followed the pr...
ORGANISM(S): Homo sapiens (Human) 
2020-10-20 | PXD020807 | Pride
Tmtpro Eclipse Atra Sps-ms3 Multi-notch Retinoic acid 
ProteomicsIsobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)
A vast assortment of human cell lines is available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, we determined the relative protein abundance profiles of a panel of eight diverse, but comm...
ORGANISM(S): Homo sapiens (Human) 
2020-10-19 | PXD020806 | Pride
Faims Tmtpro Eclipse Sps-ms3 Multi-notch Rts 
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 
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 
UnknownSeasonal Trends in Suicide Attempts-Keywords Related Searches: A Google Trends Analysis.
Not available
S-EPMC11241548 | biostudies-literature
TranscriptomicsSmall RNA sequencing of plasma RNA
We report the sequencing of small RNAs present in the plasma of three normal subjects. In addition to microRNAs we identified abundant non-human small RNA sequences. The organisms from which these were derived were identified by BLAST searches with contigs assembled from the short sequences. The tax...
ORGANISM(S): Homo sapiens 
2014-09-29 | E-GEOD-52981 | biostudies-arrayexpress
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