Skip to main content

Table 1 Available filters and parameters for simulated digests

From: PChopper: high throughput peptide prediction for MRM/SRM transition design

Type of Filter/parameter Description
Length filter Filters out peptides outside of a defined range. i.e. peptides whose length is less than Lenmin or greater than Lenmax should be filtered from the final results. This can be customized to match the requirements of a particular experiment.
Problematic residue filter Filters out peptides that contain residues that may be problematic. i.e. peptides that contain sulphur such (methionine and cysteine). Again this can be customized to match the requirements of a particular experiment.
Full dataset filter Only lists results if the specified enzyme (or enzymes) is able to produce peptides that contain all of the specified residues.
Enzyme Multiplicity Parameter Whether the simulated digest should use a single enzyme per run, or a combination of two enzymes for each run.
Phosphorylation Aware Cleaving Parameter If this value is true, cleavages that are next to phosphorylation sites are not cleaved in the simulation.
Pair-wise Digest Parameter Specifies if a pair-wise combination of enzymes should be used for each digest.