The Peptide and Protein Filter node filters PSMs according to score thresholds. It excludes any proteins, peptides, and PSMs that do not match the specified filter criteria. It also excludes all PSMs without a peptide group, all peptide groups without a PSM, and all proteins without a PSM.
This node applies a peptide confidence filter and a peptide length filter to target and decoy peptides. It marks all peptides that do not pass these filters and their associated PSMs, as well as any proteins left without any identifying PSMs, as excluded in the result file and updates the data in the Count columns. In the nodes that follow the Peptide and Protein Filter node in the workflow, you can determine whether the application processes only excluded results or all results. For example, the Protein Validator node must read all results, including the excluded results, to obtain a a fair distribution of identifications, but the Protein Grouping node does not consider excluded results.
Peptide confidence filters filter by confidence, but PSM filters filter by association with the peptides. The application therefore allows PSMs to pass when it should exclude them, undermining the criteria for peptide confidence. For example, if you set the peptide confidence filter to High, the application filters out peptides with lower confidence, but it allows PSMs with lower confidence to pass.
The following table describes the parameters for the Peptide and Protein Filter node.
Parameter | Definition |
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Peptide Confidence at Least | Excludes peptides with a low confidence level from the peak detection results.
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Keep Lower Confident PSMs | Determines whether to retain or discard PSMs with a lower confidence than the specified peptide confidence in the final results.
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Minimum Peptide Length | Determines whether to include or exclude peptides shorter than this value in the results. Range: 4 amino acids–no maximum number of amino acids Default: 6 amino acids |
Remove Peptides Without Protein Reference | Determines whether to include or exclude all peptides and PSMs from the results that have no protein reference after the application applies the protein filter.
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Minimum Number of Peptide Sequences | Specifies the minimum number of different peptides that proteins must have for the application to include them in the final results. Range: 1–no maximum; default: 1 |
Count Only Rank 1 Peptides | Determines whether to include or exclude proteins from the results on the basis of the rank of the peptides.
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Count Peptides Only for Top Scored Protein | Determines whether to include or exclude proteins from the results on the basis of the number of peptide sequences.
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