The Tag to Annotated Proteoform Search node performs a sequence tag search first and then sends all the results from the sequence tag search to an annotated proteoforms search. The sequence tag search reduces the amount of spectra searched by the annotated proteoform search step and reduces the overall search time for large data.
The following table lists the parameters for the 4.4 version of the node. For information about the 3.0 version, refer to the user interface.
Parameter | Description |
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1. Input Data | |
Input Database | Specifies the name of the database to search. |
2a. Sequence Tag | |
Minimum Tag Score | Minimum probability that the probable tag is not found by chance. |
Amino Acid Gap | Largest number allowed of sequential amino acids not having a fragment between them. |
Max Tags | Greatest number of probable tags considered for each search per target. |
Minimum Fragments Used | Minimum number of fragments required for each sequence tag. |
Remove Water Losses | When set to True, water loss is not considered when searching sequence tags. |
Consider Isobaric Dipeptide Gaps | When set to True, for example, both GA and Q are considered for gaps of 128.0 Da. |
Compiler Tolerance | The permissible error, measured in ppm between two fragment ion masses that are still considered as matching an amino acid |
2b. Annotated Proteoform (Absolute Mass) Search | |
Fragment Mass Tolerance | Specifies the mass tolerance in Da or ppm used for matching fragment peaks. Range: 0–2.0 Da; 1–50 ppm |
Maximum PTMs per Isoform | Limits the number PTMs to add to any given proteoform. If more than this number of PTMs are present on an isoform, the proteoforms created are limited to the ones with combinations of PTMs having this many PTMS or fewer. |
Maximum SNPs per Isoform | Limits the number SNPs to add to any given proteoform. If more than this number of SNPs are present on an isoform, the proteoforms created are limited to the ones with combinations of SNPs having this many SNPs or fewer. |
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. |
N-Term Modifications to Include | Selected modifications are included on all intact proteoforms n-termini. |
Delta M Mode | Determines whether the application conducts the search in Delta M (Δm) Mode. For more information on this mode, see Delta M Mode searches. |
Calculate FDR | Specifies whether the FDR is calculated. You might see fewer results passing the FDR threshold if you use Delta M Mode. |
Decoy Reps | The number of times a decoy search is run. A higher number of repetitions produces more stable decoy results but increases search times. |
Maximum PrSMs per Precursor | Maximum number of PrSMs matched per precursor limits the number of results to the highest scoring hits. |
Minimum Matched Fragments | Return only hits with this many or more matched fragments. |
Random Seed Value | User settable advanced parameter that ensures that the FDR calculation is reproducible in repeat runs. |
3. Static (Fixed) Modifications | |
Static (Fixed) Modification | Specifies a static (also known as fixed) modification from a list of known modifications. Static modifications apply universally to every instance of the specified residues. |
4. Multithreading Options | |
CPU Usage | The amount of CPU to direct to data processing:
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5. Fragmentation Method | |
Override Fragmentation Method | Manually set the fragmentation method. Auto: allows the software to determine the correct fragmentation type. (Default) |
6. UVPD Method | |
Default UVPD Method | Set the number of ion types to consider for the score of UVPD fragment ion spectra:
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