The following table describes the parameters on the left side of the Identification page.

Identification page parameters

Parameter

Description

Sequence Matching Mass Tolerance

Specifies the mass tolerance (in ppm or Da) within which the mass of the full sequence and individual components must fall to be considered a match.

Enable Drug-to-Antibody Ratio (checkbox)

(Protein only) Prompts the application to determine the average drug-to antibody ratio (DAR) value based on the drug load assignments to the identifications. You must select a modification candidate.

Select a variable modification candidate for the DAR calculation

(Protein only) These parameters show the information for the selected variable modification candidate.

List of Modifications (drop-down list)

(Enabled only when you select the Enable Drug-to-Antibody Ratio checkbox) Lists all of the side chain variable modifications available in the Protein Sequence Editor.

An N-terminal or a C-terminal modification that is not already included as a side chain modification is not available in this list. If you want to select a missing modification, first add it as a custom modification to the list of side chain modifications using the Protein Sequence Editor. See Assigning modifications to a protein sequence.

Select one modification from this list to be the drug linker. The residue, monoisotopic mass, and average mass information for the selected modification appears.

When you select a drug linker from this list, after the application finishes the matched sequence identification step, it automatically searches for all of the modifications that match the selected drug linker and then reports the number of matched modifications as the Drug Load value on the deconvoluted spectra and in the Matched Sequence pane of the Process and Review page.

If you select the Enable Drug-to-Antibody Ratio checkbox but do not select a modification from this list, the following occurs:

  • If you manually process the experiment, the application displays an error message informing you that a modification selection is required.
  • If you automatically process the experiment, the application does not display an error message, but the resulting drug load values appear as 0.

Residue

(Not editable) Residue of the selected modification.

Monoisotopic Mass

(Not editable) Monoisotopic mass of the selected modification.

Average Mass

(Not editable) Average mass of the selected modification.

Multiconsensus Component Merge

These parameters control the merging of the deconvoluted results for multiple raw data files when you select Multiconsensus as the result format on the Intact Mass Analysis page.

Deconvolution Mass Tolerance

Specifies the mass tolerance (in ppm or Da) that components from individual raw data files must meet to be merged into a multiconsensus component.

The application excludes individual raw data file components whose masses differ by more than this tolerance from a multiconsensus component.

RT Tolerance

Specifies the maximum difference in retention time (RT) that components from individual files must meet to be merged into a multiconsensus component.

The application excludes individual raw data file components whose retention times are separated by more than this gap from a multiconsensus component.

Minimum Number of Required Occurrences

Specifies the minimum number of individual raw data files that must be included in a multiconsensus component for it to be considered valid.

The application excludes multiconsensus components comprised of fewer than this number of files.