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Identification of human membrane proteins

ABSTRACT: Typically, integral membrane and membrane associate proteins are underrepresented in proteomic experiments due to their low abundance and solubility during sample preparation. We collected two fractions upon cell lysis, one comprising the insoluble membrane fraction the other the soluble cytosolic fraction. Using detergents and additives we were able to release the proteins from the membrane fraction and subsequently perform trypsin digestion for analysis.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Hela Cell

SUBMITTER: Andreas Schmidt

LAB HEAD: Axel Imhof

PROVIDER: PXD005063 | Pride | 2019-02-25

REPOSITORIES: Pride

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Publications

Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets.

Ammar Constantin C Berchtold Evi E Csaba Gergely G Schmidt Andreas A Imhof Axel A Zimmer Ralf R

Journal of proteome research 20190308 4

Spectral libraries play a central role in the analysis of data-independent-acquisition (DIA) proteomics experiments. A main assumption in current spectral library tools is that a single characteristic intensity pattern (CIP) suffices to describe the fragmentation of a peptide in a particular charge state (peptide charge pair). However, we find that this is often not the case. We carry out a systematic evaluation of spectral variability over public repositories and in-house data sets. We show tha ...[more]

PMID: 30793903

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