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 comes with plenty of documentation. Have a start with the package documentation page
?synapter and the vignette
Do not hesitate to contact me for questions/comments/suggestions.
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.
synapter is available from the Bioconductor repository. The package and its dependencies can be installed with
See also the
synapter Bioconductor page for on-line access to the vignette and the reference manual.
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