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The ProCan90 HEK293 dataset - A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs

ABSTRACT: A collection of HEK293 SWATH-MS raw data files generated as part of the routine operation of the ProCan experimental facility. These files represent technical replicates each being an aliquot from the same pooled digest, with fifteen runs collected from each of the six Sciex Triple TOF 6600 mass spectrometers, giving a total of 90 raw data files.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Early Embryonic Cell, Embryonic Stem Cell, Kidney

SUBMITTER: Sean Peters

LAB HEAD: Roger Reddel

PROVIDER: PXD011093 | Pride | 2019-04-11

REPOSITORIES: Pride

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A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs.

Peters Sean S Hains Peter G PG Lucas Natasha N Robinson Phillip J PJ Tully Brett B

Journal of proteome research 20190130 3

In the current study, we show how ProCan90, a curated data set of HEK293 technical replicates, can be used to optimize the configuration options for algorithms in the OpenSWATH pipeline. Furthermore, we use this case study as a proof of concept for horizontal scaling of such a pipeline to allow 45 810 computational analysis runs of OpenSWATH to be completed within four and a half days on a budget of US $10 000. Through the use of Amazon Web Services (AWS), we have successfully processed each of ...[more]

PMID: 30652484

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