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Proteomics in Systems Biology pp 219–232Cite as

Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1394))

Abstract

Mass spectrometry-based methods allow for the direct, comprehensive analysis of expressed proteins and their quantification among different conditions. However, in general identification of proteins by assigning experimental mass spectra to peptide sequences of proteins relies on matching mass spectra to theoretical spectra derived from genomic databases of organisms. This conventional approach limits the applicability of proteomic methodologies to species for which a genome reference sequence is available. Recently, RNA-sequencing (RNA-Seq) became a valuable tool to overcome this limitation by de novo construction of databases for organisms for which no DNA sequence is available, or by refining existing genomic databases with transcriptomic data. Here we present a generic pipeline to make use of transcriptomic data for proteomics experiments. We show in particular how to efficiently fuel proteomic analysis workflows with sample-specific RNA-sequencing databases. This approach is useful for the proteomic analysis of so far unsequenced organisms, complex microbial metatranscriptomes/metaproteomes (for example in the human body), and for refining current proteomics data analysis that solely relies on the genomic sequence and predicted gene expression but not on validated gene products. Finally, the approach used in the here presented protocol can help to improve the data quality of conventional proteomics experiments that can be influenced by genetic variation or splicing events.

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Acknowledgement

Our work was supported by the German Ministry for Education and Research (BMBF, grant number 0315082, 01EA1303 to S.S.), the European Union (FP7/2007-2013), under grant agreement n° 262055 (ESGI), and the Max Planck Society. This work is part of the Ph.D. thesis of T.L.

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Authors and Affiliations

  1. Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany

    Toni Luge & Sascha Sauer

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  1. Toni Luge
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  2. Sascha Sauer
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Corresponding author

Correspondence to Sascha Sauer .

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Editors and Affiliations

  1. University of Regensburg Institute of Functional Genomics, Regensburg, Germany

    Jörg Reinders

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Luge, T., Sauer, S. (2016). Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing. In: Reinders, J. (eds) Proteomics in Systems Biology. Methods in Molecular Biology, vol 1394. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3341-9_16

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  • DOI: https://doi.org/10.1007/978-1-4939-3341-9_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3339-6

  • Online ISBN: 978-1-4939-3341-9

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