R: Combine label-free data for optimal identification and...
synapter-package
R Documentation
Combine label-free data for optimal identification and quantitation
Description
The synapter package provides functionality to reanalyse label-free
proteomics data acquired on a Synapt G2 mass spectrometer. One or several
runs, possibly processed with additional ion mobility separation to
increase identification accuracy can be combined to other quantitation
files to maximise identification and quantitation accuracy.
Details
Three pipelines of variying flexibility are proposed the preform data
analysis: (1) a graphical user interface is provided through the
synatperGUI function, (2) the synergise function is a
single entry function for a complete analysis and (3) low level,
step-by-step data processing can be achieved as described in
?Synapter.
A high-level overview of the package and how to operate it can be
found in the vignette, accessinble with
synapterGuide(). Detailed information about the data processing
can be found in the respective function and class manual pages
appropriately referenced in the vignette.
For questions, use the Biocondcutor mailing list or contact the
author. The vignette has a section with details on where/how to get
help.
Author(s)
Laurent Gatto, Pavel V. Shliaha and Nick J. Bond
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
References
Improving qualitative and quantitative performance for MSE-based label
free proteomics, N.J. Bond, P.V. Shliaha, K.S. Lilley and L. Gatto,
J Proteome Res. 2013 Jun 7;12(6):2340-53. doi: 10.1021/pr300776t. PubMed PMID: 23510225.
The Effects of Travelling Wave Ion Mobility Separation on Data
Independent Acquisition in Proteomics Studies, P.V. Shliaha, N.J. Bond,
L. Gatto and K.S. Lilley, J Proteome Res. 2013 Jun 7;12(6):2323-39. doi: 10.1021/pr300775k.
PMID: 23514362.