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### 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. Installation of the package requires `R` version 2.15.1 (the latest stable release). The package and its dependencies can be installed source("") 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 (user name: `readonly`, password: `readonly`)