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524D / compareMS2

Compare samples by MS2 spectra
MIT License
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SDRF support for CLI and GUI #51

Open magnuspalmblad opened 12 months ago

magnuspalmblad commented 12 months ago

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

magnuspalmblad commented 6 months ago

SDRF is available in both a tab-delimited version and a JSON function. I suggest allowing either of these to be used as the samples to species file. The tooltip in the GUI should reflect that an SDRF or tab delimited file (as currently supported).