Rost2014sgs: SWATH-MS Gold Standard Dataset

In UCLouvain-CBIO/msdata2: Data accompanying the Benchmarking package

Description

The SWATH-MS Gold Standard (SGS) dataset consists of 90 SWATH-MS runs of 422 synthetic stable isotope-labeled standard (SIS) peptides in ten different dilution steps (1, 2, 4, 8, ..., 512 times), spiked into three protein backgrounds of varying complexity (water, yeast and human), acquired in three technical replicates. The SGS dataset was manually annotated, resulting in 342 identified and quantified peptides with three or four transitions each. In total, 30,780 chromatograms were inspected and 18,785 were annotated with one true peak group, whereas in 11,995 cases no peak was detected.

See also http://www.openswath.org/openswath_data.html for details.

Usage

data(Rost2014sgsHuman)
data(Rost2014sgsYeast)
data(Rost2014sgsWater)

Format

The data is an instance of class MSnSet from package MSnbase.

Source

SWATH-MS Gold Standard Dataset

References

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. Nat Biotechnol. 2014 Mar;32 (3):219-23. doi: 10.1038/nbt.2841. (PubMed)

Examples

library(msdata2)
data(Rost2014sgsHuman)
Rost2014sgsHuman
pData(Rost2014sgsHuman)
head(exprs(Rost2014sgsHuman))

UCLouvain-CBIO/msdata2 documentation built on July 4, 2020, 10:15 p.m.