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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 
ProteomicsThe choice of search engine affects sequencing depth and 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) 
2021-08-10 | PXD025655 | Pride
Search engines Fdr Immunopeptidomics 
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
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
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 
ProteomicsSynthetic (Phospho)Peptide Library
The submitted dataset contains raw files from 96 synthetic peptide libraries, using either HCD or ETD as fragmentation technique. The synthesized 96 tryptic peptide libraries containing >100,000 unmodified peptides plus their corresponding >100,000 phosphorylated counterparts with precisely known s...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-04-14 | MSV000091718 | MassIVE
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-02 | MSV000082567 | MassIVE
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 
UnknownThe Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires.
Not available
S-EPMC8724928 | biostudies-literature
UnknownA novel algorithm for validating peptide identification from a shotgun proteomics search engine.
Not available
S-EPMC3608465 | biostudies-literature
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