Requires experimental data, type of spectral processing tool used, and acquisition type. Additionally, the columns containing the protein name and modifications must be indicated
globalConverterPTM( data.ptm, data.protein = NULL, annotation = NULL, modification.column, processing.tool, acquisition.type )
data.ptm | data containing modifications from spectral processing tool |
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data.protein | data containing unmodified peptides from spectral processing tool |
annotation | annotation file if required by MSstats converter. Please view documentation from MSstats or MSstatsTMT for your specific tool. |
modification.column | string of column name containing modification information for data.ptm dataset. |
processing.tool | name of spectral processing tool for data. Must by one of "SKYLINE", "PROGENESIS", "SPECTRONAUT", "PD", "OPENMS", "OPENSWATH". |
acquisition.type | string of "LabelFree" or "TMT". For non-TMT experiments please use "LabelFree" |