synapter-package.RdThe synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.
Two pipelines of variying flexibility are proposed the preform data
analysis: (1) the synergise1 and synergise2 function are
single entry functions for a complete analysis and (2) low level,
step-by-step data processing can be achieved as described in
?Synapter.
A high-level overview of the package and how to operate it can be
found in the vignette, accessinble with
synapterGuide(). Detailed information about the data processing
can be found in the respective function and class manual pages
appropriately referenced in the vignette.
For questions, use the Biocondcutor mailing list or contact the author. The vignette has a section with details on where/how to get help.
Improving qualitative and quantitative performance for MSE-based label free proteomics, N.J. Bond, P.V. Shliaha, K.S. Lilley and L. Gatto, J Proteome Res. 2013 Jun 7;12(6):2340-53. doi: 10.1021/pr300776t. PubMed PMID: 23510225.
The Effects of Travelling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies, P.V. Shliaha, N.J. Bond, L. Gatto and K.S. Lilley, J Proteome Res. 2013 Jun 7;12(6):2323-39. doi: 10.1021/pr300775k. PMID: 23514362.