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ProteomicsHistione HCD and CID datasets for evaluation of search engines
To identify confident spectra from histone peptides containing PTMs, we present a method in which one kind of modification is searched each time. We then combine the identifications of multiple search engines to obtain confident results. We find that two search engines, pFind and Mascot, identify mo...
ORGANISM(S): Homo sapiens (Human) 
2014-09-01 | PXD001118 | Pride
Proteomics Search engine Post-translational modification Data analysis Histone 
ProteomicsPeptideForest: Semi-supervised machine learning integrating multiple search engines for peptide identification
We introduce PeptideForest, a semi-supervised machine learning approach that integrates the assignment of peptides to mass spectra from multiple algorithms to train a random forest classifier, thereby combining the results from different search engines. PeptideForest increases the number of peptide-...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2025-06-02 | PXD056915 | Pride
Human Machine learning E. coli Statistical post-processing Peptide identification 
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
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 
UnknownUniScore, a Unified and Universal Measure for Peptide Identification by Multiple Search Engines.
Not available
S-EPMC12272588 | biostudies-literature
ProteomicsCardiac myofilament isoforms - Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches
Purpose: The identification of protein isoforms in complex biological samples is challenging. We, therefore, used a mass spectrometry (MS) approach to unambiguously identify cardiac myofilament protein isoforms based on the observation of a tryptic peptide consisting of a sequence unique to a partic...
ORGANISM(S): Rattus norvegicus (Rat) 
2014-08-28 | PXD000874 | Pride
Multiple search engines Bioinformatics Cardiomyocyte Sarcomere Protein isoforms Rat cardiac tissue Myofilament proteome Protein sub-isoforms Lc-ms/ms 
UnknownEvaluation of proteomic search engines for the analysis of histone modifications.
Not available
S-EPMC4184451 | biostudies-literature
UnknownRefining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.
Not available
S-EPMC3717168 | biostudies-literature
UnknownDeep Learning-based MSMS Spectra Reduction in Support of Running Multiple Protein Search Engines on Cloud.
Not available
S-EPMC8382039 | biostudies-literature
UnknownFDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.
Not available
S-EPMC3707089 | biostudies-literature
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