Proteomics

Dataset Information

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Stability of peptide fragmentation patterns

ABSTRACT: Our study aims to determine the stability of fragmetnation patterns of peptides upon collision-induced dissociation (CID). Recent studies reported that for a minority of peptides, CID fragmentation leads to non-reproducible fragmentation spectra and therefore impaired identification. In order to study the fragmentation behavior, we first identified peptides that exhibit different fragmentation patterns. In order to reveal the cause, we selected a subset of the peptides and studied the dependency of abundance of distinct fragmentation patterns with collision energy settings and with of the isolation window.

INSTRUMENT(S): TripleTOF 5600+

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture, Epithelial Cell

DISEASE(S): Cervix Carcinoma

SUBMITTER: Andreas Schmidt  

LAB HEAD: Axel Imhof

PROVIDER: PXD006691 | Pride | 2019-02-25

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
2010130_TT6600_HCL_3ug_01_IDA_long.wiff Wiff
2010130_TT6600_HCL_3ug_01_IDA_long.wiff.scan Wiff
2010208_TT6600_HeLaCL_Pierce_1ug_01_IDA_long-Copy.wiff Wiff
2010208_TT6600_HeLaCL_Pierce_1ug_01_IDA_long.wiff Wiff
2010208_TT6600_HeLaCL_Pierce_1ug_01_IDA_long.wiff.scan Wiff
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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]

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