Sort   by:  
 Page size 
MetabolomicsMAVEN2: An Updated Open-Source Mass Spectrometry Exploration Platform

MAVEN, an open-source software program for analysis of LC-MS metabolomics data, was originally released in 2010. As mass spectrometry has advanced in the intervening years, MAVEN has been periodically updated to reflect this advancement. This manuscript describes a major update to the program, MA...

2024-07-22 | MTBLS3097 | MetaboLights
ProteomicsModification localization and quality control for open database search results
Open (mass tolerant) search of tandem mass spectra shows great potential in the comprehensive detection of post-translational modifications in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms f...
ORGANISM(S): Homo Sapiens 
2019-01-17 | PXD012394 |
GenomicsOptimal settings of mass spectrometry open search strategy for higher confidence
Optimal settings of mass spectrometry open search strategy for higher confidence
PRJNA448556 | ENA
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
ProteomicsOpen search strategy for inferring the masses of cross-link adducts
Development of new reagents for protein cross-linking is continually ongoing. The chemical formulas of the linker adducts formed by these reagents are usually deduced from expert knowledge, and then validated by mass spectrometry. Clearly, it would have been more rigorous if the adduct masses are ...
ORGANISM(S): Bos taurus (Bovine) 
2021-09-09 | PXD020704 | Pride
Modifications Xl-ms Emcs Open search Cross-linking Mass spectrometry Glutaraldehyde 
TranscriptomicsOptimal settings of mass spectrometry open search strategy for higher confidence
More than half of the mass spectra could not be identified in most proteome mass spectrometry experiments. Various modifications have been considered as a major reason. Open search strategy was then introduced to solve this problem, however, lacking thorough quality assessment using independent info...
ORGANISM(S): Homo sapiens 
2018-10-04 | GSE112623 | GEO
TranscriptomicsGenome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was tr...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress
ProteomicsA systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines
Background: Liquid chromatography- tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventio...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2021-03-11 | MSV000087034 | MassIVE
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-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue
In recent years, high-throughput technologies have contributed to development a more precise picture of the human proteome. However, 2,129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, low-molecular-weight (LM...
ORGANISM(S): Homo sapiens (Human) 
2019-11-04 | PXD015759 | Pride
Testis Open-pfind，efficiency Chromosome-centric human proteome project Missing proteins 
Sort   by:  
 Page size