itraqdata is and example data sets is an iTRAQ 4-plex
experiment that has been run on an Orbitrap Velos instrument. It
includes identification data in the feature data slot obtain from the
Mascot search engine. It is a subset of an spike-in experiment where
proteins have spiked in an Erwinia background, as described in
Karp et al. (2010), Addressing accuracy and precision issues in iTRAQ quantitation, Mol Cell Proteomics. 2010 Sep;9(9):1885-97. Epub 2010 Apr 10. (PMID 20382981).
The spiked-in proteins in
itradata are BSA and ENO and are
present in relative abundances 1, 2.5, 5, 10 and 10, 5, 2.5, 1 in the
114, 115, 116 and 117 reporter tags.
msnset object is produced by running the
method on the
itraqdata experimental data, as detailed in the
quantify example. This example data set is used in the
MSnbase-demo vignette, available with
msnset2 object is another example iTRAQ4 data that is used
to demonstrate features of the package, in particular the
feature aggregation method, described in
corresponds to 11 proteins with spectra measurements from the original
data set described by Breitwieser et al. (2011) General
statistical modeling of data from protein relative expression isobaric
tags. J. Proteome Res., 10, 2758-2766.
1 2 3 4 5 6 7 8 9 10
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