By default, the Host Cell Protein subpage of the processing method wizard is inactive. To edit the parameters on this page, select the Enable HCP checkbox.
The Host Cell Protein subpage includes eight sections: Basic Parameters, Protease Parameters, Identification Filters, Static Modification, Variable Modification, Protein Terminal Modification, Peptide Terminal Modification, and Advance Parameters.
| No. | Description | No. | Description |
|---|---|---|---|
1 | Parameters tab (processing method editing wizard) | 7 | Static Modification area |
2 | Subpage navigation bar | 8 | Variable Modification area |
3 | Enable HCP checkbox | 9 | Protein Terminal Modification area |
4 | Basic Parameters area | 10 | Peptide Terminal Modification area |
5 | Protease Parameters area | 11 | Advance Parameters area |
6 | Identification Filters area |
The table below describes the parameters on the Host Cell Protein subpage.
Parameter | Description |
|---|---|
Basic Parameters | |
Protein Database (dropdown list) | Specifies the protein FASTA database to use in the HCP search.
Note: If you add or delete a database in the Host Cell Protein Database Manager, this list will update to reflect any changes. |
Acquisition Type (dropdown list) | Specifies the data acquisition type.
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Precursor Mass Tolerance (ppm) | Specifies the precursor mass tolerance.
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Ions to Search | Specifies which fragment ions to search by selecting the appropriate checkboxes:
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Mass Range (MH+peptide mass range to analyze) | Specifies the mass range of peptides to search.
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Protease Parameters | |
Select Protease (dropdown list) | Specifies the appropriate protease.
To the right of the Select Protease drop-down menu, the N-Term and C-Term boxes are read-only and display the activity of the selected protease at the N- and C-terminals. |
Protease Termini | Specifies the digestion at the protease termini.
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Max Num Internal Miscleavages | Specifies the maximum number of internal miscleavages.
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Enabled Decoy Search | Specifies if the application performs a decoy search to reduce false HCP matches found in the databases.
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Identification Filters | |
E-Value Cutoff (checkbox) | Select the E-Value Cutoff checkbox to apply a quality match score to refine the HCP search results. Only results with an E-value greater than or equal to the specified cutoff will be shown.
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Static Modification | |
Peptide N-/C-Terminal | In this section, you can select up to four static N- or C-terminal modifications (two modifications per N- or C-terminal) from the dropdown list. |
Static Side Chain Modification | In this section, you can select up to four static side chain modifications from the dropdown list. This modification list excludes N-glycans. To the right, in the second dropdown list, you can select the appropriate amino acid for the modification.
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Variable Modification | |
Max # of variable modifications per peptide | In the "Max # of variable modifications per peptide" box, specify the maximum number of variable modifications per peptide.
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Variable Side Chain Modification | In this section, you can select up to four variable side chain modifications from the dropdown list. This modification list excludes N-glycans. To the right, in the second dropdown list, you can select the appropriate amino acid for the modification. |
Protein Terminal Modification | |
N-/C-Terminal | In this section, you can select up to six protein terminal modifications (three modifications per N- or C-terminal) from the dropdown list. |
Peptide Terminal Modification | |
N-/C-Terminal | In this section, you can select up to six peptide terminal modifications (three modifications per N- or C-terminal) from the dropdown list. |
Advance Parameters | |
Enable Methionine Protein N-Terminal Clip | Specifies if the application removes N-terminal methionine residues before performing the HCP database search.
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