Proteomics

Dataset Information

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Comparison of fractionation proteomics for local SWATH library building


ABSTRACT: For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS-PAGE fractionation, peptide high-pH RP-HPLC fractionation and MS-acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Elisabeth Govaert  

LAB HEAD: Prof. Dr. Apr. Dieter Deforce

PROVIDER: PXD006190 | Pride | 2017-07-04

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Lib_DDA.dat Other
Lib_GP.dat Other
Lib_Gel.dat Other
Lib_RPRP.dat Other
Library_DDA_diff_R1.wiff Wiff
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Publications

Comparison of fractionation proteomics for local SWATH library building.

Govaert Elisabeth E   Van Steendam Katleen K   Willems Sander S   Vossaert Liesbeth L   Dhaenens Maarten M   Deforce Dieter D  

Proteomics 20170801 15-16


For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with  ...[more]

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