FAQ

Does Quandenser output a list of MS/MS spectra from features that are likely differentially abundant?

Quandenser does not output a list of differentially abundant MS/MS spectra. However, using the python script at bin/get_spectrum_quants.py you can obtain a tab separated file with intensities per run for each consensus spectrum, together with the feature-match probabilities, e.g.:

python get_spectrum_quants.py Quandenser_output/Quandenser.feature_groups.tsv --file_list_file file_list.txt --out_file spectrum_quants.tsv

This you could load into your statistics program of choice (R, Perseus, Excel), optionally run some kind of missing value imputation and finally apply the statistical test of choice (T-test, Welch-test, SAM).

I searched the consensus spectra with my favorite search engine. How do I map those results back to MS1 feature groups?

Using the python script in the question above, you can quickly obtain the abundances and match-probabilities per run for a given consensus spectrum.

If you want more detailed information, the mapping from consensus spectra to feature groups can be done by searching for the spectrum ID in the Quandenser.feature_groups.tsv in the last column. A detailed description of the format for this output file can be found here: https://github.com/statisticalbiotechnology/quandenser/wiki/Output-formats