The following table describes the CHIMERYS On Ardia Server parameters.

CHIMERYS On Ardia Server parameters

Parameter

Description

Processing Mode

Specifies how files should be processed by CHIMERYS.

  • One Job for All Files: All files are processed together in a single CHIMERYS job.
  • One Job per File: Each input file is processed in a single processing job. Fractionated data is handled as one file.
  • One Job per File in Fraction: Each job in a fraction is processed in its own processing job.

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;
Maximum = (unchecked)

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.
- 'None': no feature traces are stored.
- 'All': all feature traces are stored.