The following table describes the CHIMERYS On Ardia Server parameters.
Parameter | Description |
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Processing Mode | Specifies how files should be processed by CHIMERYS.
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Protein Database | Specifies the sequence database(s) to be searched. |
Prediction Model | Specifies the prediction model used for the CHIMERYS search. |
CHIMERYS Inclusion File | A CHIMERYS inclusion file is a file containing a target list of known identification, which should be traced if not identified in all .raw files processed with the workflow. |
Enzyme | Specifies the reagent used for protein digestion. |
Max. Missed Cleavage Sites | Specifies the maximum number of missed internal cleavage sites per peptide. Minimum = 0; Maximum = 4 |
Min. Peptide Length | Specifies the minimum sequence length of a peptide. Minimum = 7; Maximum = 30 |
Max. Peptide Length | Specifies the maximum sequence length of a peptide. Minimum = 7; Maximum = 30 |
Max. Number Of Modification Per Peptide | Specifies the maximum number of variable modifications per peptide. Minimum = 0; Maximum = 5 |
Min. Peptide Charge | Specifies the minimum charge of peptides considered during a search. Minimum = 1; Maximum = 6 |
Max. Peptide Charge | Specifies the maximum charge of peptides considered during a search. Minimum = 1; Maximum = 6 |
Fragment Mass Tolerance | Specifies mass tolerance used for matching fragment peaks. Minimum = 0.00001 Da | 0.01 ppm; |
X. Dynamic Modification | Select any known or suspected modification. Dynamic modifications are those which may or may not be present. |
Peptide N-Terminus (Dynamic Modifications) | Select any known or suspected N-terminal modification. Dynamic modifications are those which may or may not be present. |
Peptide N-Terminus (Static Modifications) | Static modification for the N-terminus of the peptide used during the search. Static modifications are applied universally to every instance of the specified terminus. |
X. Static Modification | Select any known or suspected modification. Static modifications are applied universally to every instance of the specified residue(s). |
Target FDR (Strict) | Specifies the target false discovery rate for high confident PSMs. Minimum = 0.0; Maximum = 1.0 |
Target FDR (Relaxed) | Specifies the target false discovery rate for medium confident PSMs. Minimum = 0.0; Maximum = 1.0 |
Feature Traces to Store | Specifies the traces to store in the result file. |