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. 2009 Sep 9:3:11.
doi: 10.1186/1752-153X-3-11.

Finding one's way in proteomics: a protein species nomenclature

Hartmut Schlüter  1 , Rolf Apweiler, Hermann-Georg Holzhütter, Peter R Jungblut
Affiliations

Finding one's way in proteomics: a protein species nomenclature

Hartmut Schlüter et al. Chem Cent J. .

Abstract

Our knowledge of proteins has greatly improved in recent years, driven by new technologies in the fields of molecular biology and proteome research. It has become clear that from a single gene not only one single gene product but many different ones - termed protein species - are generated, all of which may be associated with different functions. Nonetheless, an unambiguous nomenclature for describing individual protein species is still lacking. With the present paper we therefore propose a systematic nomenclature for the comprehensive description of protein species. The protein species nomenclature is flexible and adaptable to every level of knowledge and of experimental data in accordance with the exact chemical composition of individual protein species. As a minimum description the entry name (gene name + species according to the UniProt knowledgebase) can be used, if no analytical data about the target protein species are available.

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Figures

Figure 1
Figure 1
The three main strategies in proteomics. 2-DE: two-dimensional electrophoresis; LC: liquid chromatography; n-D: n-dimensional; db: database; MS: mass spectrometry; PMF: peptide mass fingerprint; PTM: post-translational modification.
Figure 2
Figure 2
Scheme of the flow of information starting with extracellular events via receptors, transcription factors and other proteins regulating gene expression and determining synthesis and processing of protein species. IP: interacting partner biomolecules.
Figure 3
Figure 3
Protein species (sACE P12821; g-ACE P22966) derived from the angiotensin-converting enzyme gene. CaM: calmodulin.
Figure 4
Figure 4
Protein species (GAPDH P04406) derived from the GAPDH gene. Siah1: protein interacting with GAPDH.
See this image and copyright information in PMC

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