### 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 official release is the Bioconductor version, available [here](http://bioconductor.org/packages/devel/bioc/html/synapter.html). The [github page](https://lgatto.github.io/synapter/) is a useful resource that gives access to all vignettes and manuals. ### Installation `synapter` is available from the [Bioconductor](http://www.bioconductor.org) repository. The package and its dependencies can be installed with if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("synapter") ### Help `synapter` comes with plenty of documentation. Have a start with the package documentation page `?synapter` and the vignette vignette("synapter", package="synapter") 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. ### GitHub build status Current: [](https://travis-ci.org/lgatto/synapter) ### 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).