ArticleMolecular & cellular proteomics : MCP2016
proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.
Article in Molecular & cellular proteomics : MCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Combination of Proteogenomics with PeptidemBio · 2019Article
- A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.Journal of visualized experiments : JoVE · 2018Article
- Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity.Molecular & cellular proteomics : MCP · 2018Article
- How many human proteoforms are there?Nature chemical biology · 2018Article
- The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.Genome biology · 2018Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- An Accessible Proteogenomics Informatics Resource for Cancer Researchers.Cancer research · 2017Article
- Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify.Molecular & cellular proteomics : MCP · 2017Article
- Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.Cell systems · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.Journal of proteome research · 2016Article
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Authors and funding
6 authors.
Funding
Abstract
To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs)(1) within the context of the genome. proBAMsuite also includes two R packages, proBAMr and proBAMtools, for generating and analyzing proBAM files, respectively. Applying proBAMsuite to three recently published proteomics datasets, we demonstrated its utility in facilitating efficient genome-based sharing, interpretation, and integration of proteomics data. First, the interpretation of proteomics data is significantly enhanced with the rich genomic annotation information. Second, PSMs can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. Third, using the genome as a common reference, proBAMsuite facilitates seamless proteomics and proteogenomics data integration. Finally, proBAM files can be readily visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the proteomics community. Results from this study establish proBAMsuite as a useful bioinformatics framework for proteomics and proteogenomics research.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.