ArticleJournal of proteome research2014
Evaluation of proteomic search engines for the analysis of histone modifications.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Proteomic Analysis of Histone Sequence Variants and Post-translationally Modified Forms.Advances in experimental medicine and biology · 2026Review
- Chemical proteomic mapping of reversible small molecule binding sites in native systems.Trends in pharmacological sciences · 2024Review
- Epigenome-wide impact of MAT2A sustains the androgen-indifferent state and confers synthetic vulnerability in ERG fusion-positive prostate cancer.Nature communications · 2024Article
- Enhanced mapping of small-molecule binding sites in cells.Nature chemical biology · 2024Article
- Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis.Journal of proteome research · 2024Article
- Challenges and opportunities in analyzing and modeling peptide presentation by HLA-II proteins.Frontiers in immunology · 2023Article
- Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification.Journal of personalized medicine · 2021Article
- Mass Spectral Analysis of Synthetic Peptides: Implications in Proteomics.Journal of biomolecular techniques : JBT · 2021Article
- Cataloging Posttranslational Modifications in Plant Histones.Advances in experimental medicine and biology · 2021Article
- Secretomics to Discover Regulators in Diseases.International journal of molecular sciences · 2019Review
- In Vivo Metabolic Tracing Demonstrates the Site-Specific Contribution of Hepatic Ethanol Metabolism to Histone Acetylation.Alcoholism, clinical and experimental research · 2018Article
- EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data.Journal of proteome research · 2018Article
- Review
- A multicenter study benchmarks software tools for label-free proteome quantification.Nature biotechnology · 2016Article
- Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite.Journal of proteome research · 2016Article
- Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry.Current opinion in chemical biology · 2016Review
- Analysis of histone post translational modifications in primary monocyte derived macrophages using reverse phase×reverse phase chromatography in conjunction with porous graphitic carbon stationary phase.Journal of chromatography. A · 2016Article
- Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis.Journal of visualized experiments : JoVE · 2016Article
- Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells.Epigenetics & chromatin · 2016Article
- Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications.Molecular & cellular proteomics : MCP · 2015Article
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4 authors.
Funding
Abstract
Identification of histone post-translational modifications (PTMs) is challenging for proteomics search engines. Including many histone PTMs in one search increases the number of candidate peptides dramatically, leading to low search speed and fewer identified spectra. To evaluate database search engines on identifying histone PTMs, we present a method in which one kind of modification is searched each time, for example, unmodified, individually modified, and multimodified, each search result is filtered with false discovery rate less than 1%, and the identifications of multiple search engines are combined to obtain confident results. We apply this method for eight search engines on histone data sets. We find that two search engines, pFind and Mascot, identify most of the confident results at a reasonable speed, so we recommend using them to identify histone modifications. During the evaluation, we also find some important aspects for the analysis of histone modifications. Our evaluation of different search engines on identifying histone modifications will hopefully help those who are hoping to enter the histone proteomics field. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001118.
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