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ProteomicsMS Annika: A new Cross-Linking Search Engine
A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2021-05-27 | PXD022772 | Pride
Xl-ms Proteome-discoverer Ion-mobility Search-engine 
ProteomicsDataset used to guide the development of Scout and bechmark XL-MS search engines
This submission includes the raw data analyzed and search results described in our manuscript “Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics”. In this study, we develop a strategy to generate a well-controlled XL-MS standar...
ORGANISM(S): Homo sapiens (Human) 
2024-08-03 | PXD052022 | Pride
Search engine Cross-linking Ppi Benchmarking Xl-ms Fdr 
UnknownMS Annika: A New Cross-Linking Search Engine.
Not available
S-EPMC8155564 | biostudies-literature
ProteomicsBolt: A new age peptide search engine for comprehensive MS/MS sequencing through vast protein databases in minutes
The standard platform for proteomics experiments today is mass spectrometry, particularly for samples derived from complex matrices. Recent increases in mass spectrometry sequencing speed, sensitivity and resolution now permit comprehensive coverage of even the most precious and limited samples, par...
ORGANISM(S): Homo sapiens (Human) 
2019-08-29 | PXD012700 | Pride
Mutations Hela Bolt Snp 
ProteomicsGlycopeptide identification by LC-MS/MS
Automatic and rapid identification of glycopeptides by nano-uplc-ltq-ft-ms and proteomic search engine
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2016-12-23 | PXD003578 | Pride
Glycopeptide Lc-ms/ms Byonic 
ProteomicsCan we boost N-glycopeptide identification confidence? Smart collision energy choice taking into account structure and search engine
We investigated how the structural features of N-glycopeptides and the choice of the search engine influence the optimal collision energy, delivering highest identification confidence. We carried out LC-MS/MS measurements using a series of collision energies on a large set of N-glycopeptides with bo...
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Homo Sapiens (ncbitaxon:9606) 
2023-10-14 | MSV000093110 | MassIVE
UnknownProteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.
Not available
S-EPMC11621016 | biostudies-literature
UnknownCan We Boost N-Glycopeptide Identification Confidence? Smart Collision Energy Choice Taking into Account Structure and Search Engine.
Not available
S-EPMC10853973 | biostudies-literature
ProteomicsProteome-scale recombinant standard datasets for XL-MS
This submission includes the complete set of raw data generated from the analytical standard, the concept of which is described in our manuscript "Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics". In this study, we develop a ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2024-08-06 | PXD042173 | Pride
Crosslinking mass spectrometry Search engine Bioinformatics 
ProteomicsThe choice of search engine for interpretation of immunopeptidomics datasets affects the sequencing depth and the extent of detected HLA allele-specific peptide repertoires
Standardisation of Immunopeptidomics experiments across laboratories is a pressing issue within the field, and currently a variety of different methods for sample preparation and data analysis tools are applied. Here, we compared different software packages commonly used to interrogate immunopeptido...
ORGANISM(S): Homo sapiens (Human) 
2024-08-27 | PXD023202 | Pride
Immunopeptidomics Search engine 
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