The PLGS HDMSe final peptide, MSe final peptide and MSe Pep3D output files are provided as gzipped csv files and their repective full paths can be obtained with getHDMSeFinalPeptide, getMSeFinalPeptide and getMSePep3D. These can then be used directly in the respective synpater functions and methods, as read.csv automatically uncompressed the files.
An instance of class Synapter used to demonstrate ion mobility separation and peak matching in the respective synapter vignettes. The object can be created using the files available at http://proteome.sysbiol.cam.ac.uk/lgatto/synapter/data/ and the script create_synobj2.R in system.file("scripts", package = "synapterdata").
Objects of class Synapter, implented in the synapter package. The 6 instances represent triplicate run of the Universal Proteomics Standard (UPS1) 48 protein mix in an E. coli background, spiked in at 25 and 50 femtomoles.
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