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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 official release is the Bioconductor version, available [here]( The [github page]( is a useful resource that gives access to all vignettes and manuals. ### Installation `synapter` is available from the [Bioconductor]( 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]( for on-line access to the vignette and the reference manual. ### GitHub build status Current: [![Build Status](]( ### 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](