By default, the Customize Results subpage of the processing method editing wizard is inactive. To edit the parameters on this page, select the Enable Customize Results checkbox.
NOTE
The Enable Customize Results checkbox can only be selected if an appropriate protease was previously selected on the Identification subpage of the processing method editing wizard.
The protease options "Nonspecific", “No enzyme”, or any protease with cleavage sites at both the N- and C-terminals are not supported for theoretical digestion at this time. Do not use these protease options if you want to enable the Customize Results subpage.
The Customize Results subpage includes three sections: Theoretical Digestion and Alias Naming (editable), Protease Defined on Identification (read-only), and Theoretical Digestion and Alias Naming Results (populated after the Theoretical Digestion and Alias Naming parameters are entered and applied).
| No. | Description | No. | Description |
|---|---|---|---|
1 | Parameters tab (processing method editing wizard) | 5 | Theoretical Digestion parameters |
2 | Subpage navigation bar | 6 | Protease Defined on Identification area |
3 | Enablue Customize Results checkbox | 7 | Apply button |
4 | Alias Naming table | 8 | Theoretical Digestion and Alias Naming Results table (shown blank) |
The table below describes the parameters on the Customize Results subpage.
Parameter | Description |
|---|---|
Theoretical Digestion and Alias Naming | |
Theoretical Digestion and Alias Naming (table) | Enter a custom naming scheme (up to 50 characters) into the Custom Chain Alias Root column of the Theoretical Digestion and Alias Naming table to use the chain root as a naming scheme for the peptide components identified in the analysis. Once you enter an alias naming scheme and specify the Theoretical Digestion parameters, select the Apply button to generate and view the Theoretical Digestion and Alias Naming Results table on the right side of the page. |
Digested Sequence Length Constraints | Specifies the upper and lower limits of the length of the theoretical digested peptide sequences.
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Theoretical Digested Sequence Mass Range | Specifies the upper and lower limits of the masses of the theoretical digested peptide sequences.
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Number of Allowed Missed Cleavages | Specifies the maximum number of internal cleavage sites within a peptide that the protease might miss during the digestion process.
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Cleavage Specificity (drop-down menu) | Specifies the activity of the selected protease to be applied to the theoretical digestion.
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Protease Defined on Identification | |
Protease | Read-only. Specifies the protease specified for the processing method on the Identification subpage of the processing method editing wizard. Note: If you want to edit this parameter, you must edit the Identification subpage. See Identification parameters. |
N-Term/C-Term | Read-only. Displays the activity of the selected protease at the N- and C-terminals specified for the processing method on the Identification subpage of the processing method editing wizard. Note: If you want to edit this parameter, you must edit the Identification subpage. See Identification parameters. |
Apply (button) | Select the Apply button to perform the theoretical digestion and populate the Theoretical Digestion and Alias Naming Results table on the right side of the page. |
Once you enter the Theoretical Digestion and Alias Naming parameters and select the Apply button, the results of the theoretical digestion appear in the Theoretical Digestion and Alias Naming Results table on the right side of the page.
The table below describes the information in the Theoretical Digestion and Alias Naming Results table.
Column | Description |
|---|---|
Alias Name | Displays the name of a theoretical digestion component using the alias root defined in the Theoretical Digestion and Alias Naming table. For example, if “Chain1” was typed into the Custom Chain Alias Root column of the Theoretical Digestion and Alias Naming table, the theoretical digestion components listed in the Theoretical Digestion and Alias Naming Results table will appear as “Chain1_x”, where x indicates the theoretical component number. |
Selected Protein Sequence Chain Name | Indicates the default name (derived from the FASTA file) of the target protein sequence assigned to the currently open processing method. |
Sequence | Displays the amino acid sequence constituting the theoretical digestion component. |
Digested Sequence Mass | Displays the mass of the amino acid sequence constituting the theoretical digestion component. |
Start Position/End Position | Indicates the positions of the first and last residues of the theoretical digestion component within the undigested target protein sequence. |
Miscleavage | Indicates the number of miscleavages (if any) involved in producing a theoretical digestion component. The values in this column are based on the Number of Allowed Missed Cleavage Sites parameter in the Theoretical Digestion and Alias Naming section of the Customize Results page. If the value in this column is 0, no miscleavages occurred to create the theoretical digestion component. |
Digest Position | Indicates the relative position of a particular amino acid residue at which the theoretical digestion took place; based on the specific activity of the protease assigned to the theoretical digestion and intrinsically related to the theoretical component number listed in the alias name. For example, since trypsin cleaves the peptide bond between the C-terminal of a lysine (K) or an arginine (R) residue and an adjacent amino acid, for a theoretical tryptic digestion, a digest position of 8 indicates that the theoretical digestion component resulted from trypsin acting at the eighth K/R residue in the target protein sequence. For alias root “Chain1”, this theoretical component would have the alias name “Chain1_8”. |