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. |