Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1186/1756-0500-3-178
Title (Primary) Calculation of partial isotope incorporation into peptides measured by mass spectrometry
Author Fetzer, I.; Jehmlich, N. ORCID logo ; Vogt, C.; Richnow, H.H.; Seifert, J.; Harms, H.; von Bergen, M.; Schmidt, F.
Source Titel BMC Research Notes
Year 2010
Volume 3
Page From art. 178
Language englisch
Abstract Background: Stable isotope probing (SIP) technique was developed to link function, structure and activity of microbial cultures metabolizing carbon and nitrogen containing substrates to synthesize their biomass. Currently, available methods are restricted solely to the estimation of fully saturated heavy stable isotope incorporation and convenientmethods with sufficient accuracy are still missing. However in order to track carbon fluxes in microbial communities new methods are required that allow the calculation of partial incorporation into biomolecules.Results: In this study, we use the characteristics of the so-called 'half decimal place rule' (HDPR) in order to accurately calculate the partial13C incorporation in peptides from enzymatic digested proteins. Due to the clade-crossing universality of proteins within bacteria, any available high-resolution mass spectrometry generated dataset consistingof tryptically-digested peptides can be used as reference. We used a freely available peptide mass dataset from Mycobacterium tuberculosis consisting of 315,579 entries. Fromthis the error of estimated versus known heavy stable isotope incorporation from an increasing number of randomly drawn peptide sub-samples (100 times each; no repetition) was calculated. To acquire an estimated incorporation error of less than 5 atom %, about 100 peptide masses were needed. Finally, for testing the general applicability of ourmethod, peptide masses of tryptically digested proteins from Pseudomonas putida ML2 grown on labeled substrate of various known concentrations were used and13C isotopic incorporation was successfully predicted. An easy-to-use script [1] was further developed to guide users through the calculation procedure for their own data series.Conclusion: Our method is valuable for estimating13C incorporation into peptides/proteins accurately and with high sensitivity. Generally, our method holds promise for wider applications in qualitative and especially quantitative proteomics.
Persistent UFZ Identifier
Fetzer, I., Jehmlich, N., Vogt, C., Richnow, H.H., Seifert, J., Harms, H., von Bergen, M., Schmidt, F. (2010):
Calculation of partial isotope incorporation into peptides measured by mass spectrometry
BMC Res. Notes 3 , art. 178 10.1186/1756-0500-3-178