When a spectrum library is added, the application transfers the file to the server and converts it to the internal library format. In doing this, the application parses the library and extracts the library spectrum and annotations and adds a peptide match for each entry.

Usually, this annotation includes the peptide sequence, a textual encoding of the identified chemical modifications, the charge state, and other information.

You must either map the encoded modifications to modifications known in the application or map them to be ignored.

The Chemical Modifications view describes all the known modifications. To add a modification to this view, see Add chemical modifications.

Procedure

  1. In the Spectrum Library view, select an entry that has Requires Modification Mapping in the Status column.
  2. The spectral library opens in the Modification Mapping pane.
  4. Select an entry that has a caution alert as (see the following figure for an example).
  5. (Optional) Expand the modification entry to view the found amino acids.
  7. For the unmapped modification, select a known chemical modification from the dropdown list.
  8. The alert symbol no longer appears.
  10. Select Apply.