3. If you get an error while attempting to build the spectral
library, move the file “combined.pep.xml” to the same directory as the .mzML files.
4. Precursor mass analyzer and Mass Accuracy settings should
reflect the mass spectrometer and data type you are using. For
example, if your data are from a 5600 tripleTOF, set the mass
accuracy to 20. Retention time filtering should be based on the
reproducibility of retention time in your chromatographic system. For example, if you know that your peptide retention
drifts by up to 5 min, set this value to 5 min.
5. If using your own data, the enzyme and missed cleavage settings should match the settings used for the database search by
MS-Fragger in Subheading 3.1.
6. If analyzing your own data from another organism, make sure
you download the appropriate ontology here.
Fig. 3 Examples of network of enriched GO Biological Process terms produced by
ClueGO plug-in within Cytoscape. The proportions of blue and red in the circles
reflect the proportion of proteins assigned to each term that were increased or
decreased, respectively
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Jesse G. Meyer