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. 2015 Dec;12(12):1106-8.
doi: 10.1038/nmeth.3655.

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

Jian Wang  1   2 , Monika Tucholska  3 , James D R Knight  3 , Jean-Philippe Lambert  3 , Stephen Tate  4 , Brett Larsen  3 , Anne-Claude Gingras  3   5 , Nuno Bandeira  1   2   6
Affiliations

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

Jian Wang et al. Nat Methods. 2015 Dec.
No abstract available

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Conflict of interest statement

COMPETING FINANCIAL INTERESTS

S.T. is an employee of SCIEX. N.B. has an equity interest in Digital Proteomics, LLC, a company that may potentially benefit from the research results; Digital Proteomics LLC was not involved in any aspects of this research. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.

Figures

Fig. 1
Fig. 1. MSPLIT-DIA identification of peptides, proteins and protein-protein interactions
(a) Overview of the MSPLIT-DIA identification process (see also the Supplementary Note for details). (b) Peptide multiplicity as identified by MSPLIT-DIA in multiplexed spectra from DIA runs of varying complexity. (c) A human lysate was analyzed by itself (left) and with a spiked-in standard 48-protein mixture (UPS1, right); the number of unique peptides identified using six different data analysis approaches is shown. MSPLIT-DIA analysis was performed either with a library from paired Data Dependent Acquisition (DDA) runs of the same sample (green) or using the large generic SWATH-Atlas library (purple). (d) Number of peptides detected across four runs (top panel) and reproducibility analysis comparing MSPLIT-DIA and MSGFDB-DDA (bottom panel) in relation to peptide abundance (x-axis). (e) Comparison of MSGFDB-DDA and MSPLIT-DIA methods as applied in a semi-quantitative approach to detect protein-protein interactions from affinity-purified samples from two bait proteins (EIF4A2, MEPCE) and a negative control (GFP). (f) DIA analysis workflow using MSPLIT-DIA circumvents the need to use additional DDA runs, spike-in peptides or manual curation for generation of sample-specific assay libraries. (g) Results of PeakView and MSPLIT-DIA peptide quantification with or without retention-time alignment and with or without an MSPLIT-generated assay library.
See this image and copyright information in PMC

References

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