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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
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
ProteomicsPTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization co...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-01-10 | MSV000096828 | MassIVE
UnknownIdentification of modified peptides using localization-aware open search.
Not available
S-EPMC7426425 | biostudies-literature
UnknownCrystal-C: A Computational Tool for Refinement of Open Search Results.
Not available
S-EPMC7460724 | biostudies-literature
ProteomicsReliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis
Patients with cirrhosis are at a relatively high risk of developing complications, such as hepatic decompensation and hepatocellular carcinoma. Identifying cirrhosis in patients is essential in clinical practice because of the need to control disease progression and select different treatment strateg...
ORGANISM(S): Homo sapiens (Human) 
2025-07-23 | PXD055743 | Pride
Connectome strategy  proteomics  open search  post-translational modifications  peptide spectral matches 
UnknownN-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search.
Not available
S-EPMC6112209 | biostudies-literature
UnknownCompleteness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources.
Not available
S-EPMC5739406 | biostudies-literature
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