Molecular & Cellular Proteomics
ResearchExtending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues*[S]
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Author contributions: R.B., S.M., Y.B., C.E., and L.R. designed the research; R.B., S.M., and V.Z. performed the research; R.B., O.M.B., T.G., S.M.M., L.C., T.E., and L.R. contributed new reagents or analytic tools; R.B., O.M.B., L.C., and L.R. analyzed data; R.B., S.M., O.V., O.R., and L.R. wrote the paper.
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R.B. and S.M.M. acknowledge support from the Commission for Technology and Innovation, Switzerland, under the Grant No. 13539.1 PFFLI-LS.
Competing financial interests: The authors R.B., O.M.B., T.G., S.M.M., C.E., Y.B., O.R. and L.R. work for Biognosys AG.
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Bernhardt, O. M., Selevsek, N., Gillet, L. C., Rinner, O., Picotti, P., Aebersold, R., and Reiter, L. (2012) Spectronaut A fast and efficient algorithm for MRM-like processing of data independent acquisition (SWATH-MS) data. Proceedings of the 60th ASMS Conference on Mass Spectrometry and Allied Topics, 2012, Vancouver, BC, Canada.
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- APAP
acetaminophen
- ATP
adenosine triphosphate
- CV
coefficient of variation
- DIA
data-independent acquisition
- DDA
data-dependent acquisition
- FDR
false discovery rate
- HRM
hyper reaction monitoring
- iRT
indexed retention time
- NAPQI
N-acetyl-p-benzoquinone imine
- SRM
selected reaction monitoring; DIA with 32 sequential windows of 25 Dalton width.
The abbreviations used are:
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This article contains supplemental material files HRM-Spectral-libraries.xlsx, Profiling-Standard-Data-Set-table.xlsx, and Micro-tissue-Data-Set-tables.xlsx; Tables 1–5, and Figs. 1–9.
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These authors contributed to this work equally.