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ProteomicsFast open modification spectral library searching through approximate nearest neighbor indexing
Open modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to match against its unmodified variant by using a very wide precursor mass window. A drawback of this strategy, however, is that it leads to a l...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2021-05-25 | PXD009861 | Pride
Ptm Open modification searching Spectral library 
ProteomicsOpen database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching
Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation data of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag be hide. This is especially ...
ORGANISM(S): Campylobacter fetus subsp. fetus Burkholderia cenocepacia J2315 Burkholderia pseudomallei (strain K96243) Acinetobacter baumannii 
2020-06-24 | PXD018587 | Pride
Wide tolerant database searching Bacterial glycosylation Open searching Glycosylation Glycopeptides Post-translational modifications Proteomics Atypical glycosylation 
ProteomicsExtremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units
Open modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor mass window to allow modified spectra to match against their unmodified variants, after which the modification types can be inferred from the c...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2019-12-06 | PXD013641 | Pride
Proteomics Graphics processing unit Post-translational modification Mass spectrometry Feature hashing Approximate nearest neighbor indexing Spectral library Open modification searching 
MetabolomicsMetabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial D - fermented seaweed open water-dose response)

Testing the effect of seaweed as a novel cost-efficient feed source for Atlantic salmon feed. Fermentation of novel raw materials for fish feed is a new practice with little prior experience of direct relevance to aquaculture and fish farming. In Trial D, an alternative marine compound is include...

2023-06-13 | MTBLS6733 | MetaboLights
ProteomicsSimulated spectral library searching on TripleTOF phosphopeptide datasets
Synthetic phosphopeptides and enriched K562 cell phosphopeptides were analyzed using a TripleTOF 6600 mass spectrometer before and after enzymatic dephosphorylation. Dephosphorylated peptides identified by X!Tandem database searching were subjected to spectral simulation of all possible single phosp...
ORGANISM(S): Homo Sapiens (human) 
2019-12-03 | PXD012433 | JPOST Repository
ProteomicsThe application of open searching based approaches for the identification of Acinetobacter baumannii O-linked glycopeptides decorated with diverse capsule derived glycans
Protein glycosylation is being increasingly recognised as a common modification within microbial organisms, contributing to protein functionality and optimal infectivity of pathogenic species. Due to this, the interest in characterising microbial glycosylation events is increasing - requiring high-t...
ORGANISM(S): Acinetobacter baumannii ACICU Acinetobacter baumannii AB307-0294 Acinetobacter baumannii D1279779 
2021-11-02 | PXD027820 | Pride
Lc-ms Proteomics Glycopeptides 
ProteomicsHyPep: An Open-Source Software for Identification and Discovery of Neuropeptides using Sequence Homology Searching
Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases ar...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2023-02-02 | PXD037058 | Pride
Peptidomics Hypep Homology Mass spectrometry Peptide De novo sequencing Fdr Neuropeptide 
ProteomicsQuantification of Raloxifene Specific 471 Da Adducts in CYP3A4 and P450-Reductase
Drugs are often metabolized to reactive intermediates that form protein adducts. Adducts can inhibit critical proteins, elicit immune responses, and cause life threatening adverse drug reactions. The masses of metabolites are frequently unknown, rendering traditional mass spectrometry-based proteomi...
ORGANISM(S): Homo Sapiens Rattus Norvegicus 
2022-02-21 | PXD024932 | panorama
UnknownOpen Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching.
Not available
S-EPMC8143609 | biostudies-literature
TranscriptomicsCynomolgus monkey testicular cDNAs for discovery of novel human genes
BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequ...
ORGANISM(S): Homo sapiens 
2010-06-05 | E-GEOD-513 | biostudies-arrayexpress
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