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Category Text Publication
Reference Category Journals
DOI 10.1002/mas.21346
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Title (Primary) Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
Author Seifert, J.; Taubert, M.; Jehmlich, N. ORCID logo ; Schmidt, F.; Völker, U.; Vogt, C.; Richnow, H.H.; von Bergen, M.
Source Titel Mass Spectrometry Reviews
Year 2012
Volume 31
Issue 6
Page From 683
Page To 697
Language englisch
Keywords microbial ecology;functional metaproteomics;protein-stable isotope probing (protein-SIP)

The community phenotype as the sum of molecular functions of organisms living in consortia strongly depends on interactions within these communities. Therefore, the analyses of the most significant molecules in terms of the phenotype, the proteins, have to be performed on samples without disrupting the meta-species environment. Due to the increasing genomic information, proteins provide insights into a potential molecular function and the phylogenetic structure of the community. Unfortunately, the lists of identified proteins are often based first on the technical capacity of the used methods or instruments, and second on the interpretation of them by the assignment of molecular functions to proteins in databases. Especially in non-model organisms the functions of many proteins are often not known and an increasing number of studies indicate a significant amount of uncertainty. To decrease the dependency on assumptions and to enable functional insights by metaproteome approaches, the metabolic labeling from an isotopically labeled substrate can be used. Since the metabolites deriving from the substrate are very rarely species-specific, the incorporation of the stable isotope into proteins can be used as a surrogate marker for metabolic activity. The degree of incorporation can be determined accurately on the peptide level by mass spectrometry; additionally, the peptide sequence provides information on the metabolic active species. Thereby, protein-stable isotope probing (protein-SIP) adds functional information to metaproteome approaches. The classical metaproteome approaches will be reviewed with an emphasis on their attempts towards functional interpretation. The gain from functional insights into metaproteomics by using metabolic labeling of stable isotopes of carbon, nitrogen, and sulfur is reviewed with a focus on the techniques of measurement, calculation of incorporation and data processing.

Persistent UFZ Identifier
Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F., Völker, U., Vogt, C., Richnow, H.H., von Bergen, M. (2012):
Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
Mass Spectrom. Rev. 31 (6), 683 - 697 10.1002/mas.21346