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MetaProSIP protein-SIP data - MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

ABSTRACT: MetaProSIP offers an automated high-throughput solution for 13C or 15N protein-SIP experiments. Labeled peptides are identified based on their unlabeled isotopologues. It calculates incorporation of heavy isotopes (RIA), the labeling ratio (LR) between proteins as well as additional shape properties of the isotopic distribution. FeatureXML files have been created using OpenMS 1.10 using the FeatureFinderCentroided tool. Unlabeled peptides have been identified by OMSSA 2.1.9 (precursor mass tolerance 10 ppm, fragment mass tolerance 0.5 Da, FDR filtering at 2%) and mapped to the feature data using the IDMapper tool.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Uncultured Bacterium

SUBMITTER: Timo Sachsenberg

LAB HEAD: Timo Sachsenberg

PROVIDER: PXD000382 | Pride | 2014-11-27

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	15NMix_1_3_a.featureXML	Other
	15NMix_1_3_a.raw	Raw
	15NMix_1_3_b.featureXML	Other
	15NMix_1_3_b.raw	Raw
	15NMix_1_3_c.featureXML	Other

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Publications

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.

Sachsenberg Timo T Herbst Florian-Alexander FA Taubert Martin M Kermer René R Jehmlich Nico N von Bergen Martin M Seifert Jana J Kohlbacher Oliver O

Journal of proteome research 20141201 2

We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an a ...[more]

PMID: 25412983

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