The default parameters of the Subsequence search are designed to work in most situations. However, most analyses can be improved/customized by optimizing the advanced parameters listed below. For a full list of advanced parameters, see Subsequence Search node. The Advanced parameters of the Subsequence search table is a list of advanced parameters and a brief description of how they impact the Subsequence search and results.
Parameter | Description |
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Maximum PTMs per Isoform | Limits the number of PTMs that are expanded and searched during search time. For example, if an isoform has 10 PTMs in the database and the maximum is set to 4, then only proteoforms with up to 4 PTMs are searched. This improves the search time. However, in cases of highly modified proteoforms, it is advised that you increase this value. |
Maximum SNPs per Isoform | Limits the number of amino acid mutations of single nucleotide polymorphisms (SNPs) in the same way as in the Maximum PTMs per Isoform parameter. |
Maximum PTMs per Proteoform | Limits the number of PTMs that are allowed on each proteoform during search time. For example, if an isoform has 10 PTMs in the database, the maximum per isoform is set to 8, and the maximum per proteoform is set to 4, then only proteoforms (or subseqeunces) with up to 4 PTMs are searched. This improves the search time. However, in cases of highly modified proteoforms, it is advised that you increase this value. Tip: The PSDB database contains isoforms and PTMs. All proteoforms to be searched are generated at search time according to the database and parameters selected in the search nodes. For the Subsequence search, each proteoform is expanded into its subsequences, so in the Subseqeunce search it is useful to limit the PTMs at the proteoform level. |
Maximum SNPs per Proteoform | Limits the number of amino acid mutations of single nucleotide polymorphisms (SNPs) in the same way as the Maximum PTMs per Proteoform parameter. |
Remove Disulfide Bonds | Thermo Fisher Scientific recommends setting this parameter to False. You can set this parameter to True if there are annotated disulfide bonds in the search database that you want to avoid searching or when there is a known error in the disulfide bond annotation in the database. Errors in UniProt where disulfide bonds are placed on non-cysteine residues have been observed and can cause the search to crash. |
Random Seed Value | User settable advanced parameter that ensures that the FDR calculation is reproducible in repeat runs. |