Introduction
The synapter package provides functionality to re-analyse MSe label-free proteomics data acquired on a Waters Synapt Series mass spectrometer (and probably any Waters instrument). It allows to combine acquisitions that have been optimised for better identification (typically using ion mobility separation - HDMSe) and quantitation accuracy. It also allows to transfer identifications across multiple runs to reduce missing data across an experiment.
The analysis pipeline can be executed using a simple graphical user interface (started with synapterGUI()) or a high-level function synergise to produce a html report. Alternatively, or low-level interface is available (see ?Synapter).
Help
synapter comes with plenty of documentation. Have a start with the package documentation page ?synapter and the vignette
vignette("synapter", package="synapter")
Do not hesitate to contact me for questions/comments/suggestions.
PLGS processing
The raw data files produced must first be processed by Water's PLGS software to produce synapter input files. This is described in details in the vignette. Additional information with lots of screenshots can be found in these slides.
Installation
synapter is available from the Bioconductor repository. The package and its dependencies can be installed with
source("http://www.bioconductor.org/biocLite.R")
biocLite("synapter")
See also the synapter Bioconductor page for on-line access to the vignette and the reference manual.
Source code
The code on github is for sharing, testing, issue tracking and forking/pulling purposes. Although it should be in sync with the code on the Bioconductor svn server, the latter is the official repository for the working source code. Get is with
svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rols
(user name: readonly, password: readonly)