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](http://proteome.sysbiol.cam.ac.uk/lgatto/synapter/Report/index.html). Alternatively, or low-level interface is available (see `?Synapter`).
`synapter` comes with plenty of documentation. Have a start with the package documentation page `?synapter` and the vignette
Do not hesitate to contact [me](http://proteome.sysbiol.cam.ac.uk/lgatto/) 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](http://proteome.sysbiol.cam.ac.uk/lgatto/synapter/PLGS_Data_Processing.pdf).
`synapter` is available from the [Bioconductor](http://www.bioconductor.org) repository. Installation of the package requires `R` version 2.15.1 (the latest stable release). The package and its dependencies can be installed
See also the `synapter` [Bioconductor page](http://bioconductor.org/packages/devel/bioc/html/synapter.html) for on-line access to the vignette and the reference manual.
### Source code
The code on [github](https://github.com/lgatto/synapter/) is for sharing, testing, issue tracking and forking/pulling purposes. Although it should be in sync with the code on the [Bioconductor svn server](https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/), 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`)