It would be great is compareMS2 could infer parameters and input files from an SDRF file. It does not appear to be very difficult. See attached example, corresponding to Figure 3 in the compareMS2 2.0 paper. The 'comment[data file]' field can also contain the names of MGF files. The information in the "samples_to_species" file is basically just the "comment[data file]" and "characteristics[organism]" columns of the SDRF file. The maximum difference in precursor mass could be set to the maximum of the values in the "comment[precursor mass tolerance]" column (should hopefully be the same). The rest of the parameters can be left at their defaults.
SDRF files can have additional columns, but these three are all mandatory.
Figure_3.sdrf.txt
It would be great is compareMS2 could infer parameters and input files from an SDRF file. It does not appear to be very difficult. See attached example, corresponding to Figure 3 in the compareMS2 2.0 paper. The 'comment[data file]' field can also contain the names of MGF files. The information in the "samples_to_species" file is basically just the "comment[data file]" and "characteristics[organism]" columns of the SDRF file. The maximum difference in precursor mass could be set to the maximum of the values in the "comment[precursor mass tolerance]" column (should hopefully be the same). The rest of the parameters can be left at their defaults.
SDRF files can have additional columns, but these three are all mandatory.
Figure_3.sdrf.txt