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Proteome analysis of Jurkat cells for spectral library

ABSTRACT: In order to increase the spectral library to study the ocurrence of distinct peptide fragmetation patterns, we analyzed the whole cell proteome of Jurkat cells.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture, Permanent Cell Line Cell

SUBMITTER: Andreas Schmidt

LAB HEAD: Axel Imhof

PROVIDER: PXD005111 | 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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