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customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.

Wang X, Zhang B - Bioinformatics (2013)

Bottom Line: Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification.More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific.Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Vanderbilt-Ingram Cancer Center and Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

ABSTRACT

Unlabelled: Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

Availability and implementation: customProDB and related documents are freely available at http://bioconductor.org/packages/2.13/bioc/html/customProDB.html.

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Schematic overview of the customProDB package
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btt543-F1: Schematic overview of the customProDB package

Mentions: Figure 1 illustrates the overall structure of the package. Methods and functions implemented in the customProDB package are described in detail in a tutorial available as online Supplementary Material (Supplementary File 1). In section 2, we briefly present the main functionalities of the customProDB package.Fig. 1.


customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.

Wang X, Zhang B - Bioinformatics (2013)

Schematic overview of the customProDB package
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3842753&req=5

btt543-F1: Schematic overview of the customProDB package
Mentions: Figure 1 illustrates the overall structure of the package. Methods and functions implemented in the customProDB package are described in detail in a tutorial available as online Supplementary Material (Supplementary File 1). In section 2, we briefly present the main functionalities of the customProDB package.Fig. 1.

Bottom Line: Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification.More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific.Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Vanderbilt-Ingram Cancer Center and Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

ABSTRACT

Unlabelled: Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

Availability and implementation: customProDB and related documents are freely available at http://bioconductor.org/packages/2.13/bioc/html/customProDB.html.

Show MeSH