The Annotated Proteoform Search node performs a ProSight-annotated proteoform search.
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 | Select the name of the database to search. |
2. Annotated Proteoform (Absolute Mass) Search | |
Precursor Mass Tolerance | Specifies the mass tolerance in Da or ppm used to find peak candidates. Range: 0.0–1 000 000 Da; 0.1–1000 ppm |
Fragment Mass Tolerance | Specifies the mass tolerance in Da or ppm used for matching fragment peaks. Range: 0–2.0 Da; 1–50 ppm |
Candidate Source | Specify particular proteoforms to consider for your search.
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Maximum PTMs per Isoform | Limits the number of 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 of 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. |
Maximum PTMs per Proteoform | Limits the number of 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. |
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. |
Maximum Mass to Include PTMs | Maximum proteoform mass to search with PTMs. |
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. |
Remove Redundant Delta M Hits | This parameter controls the results returned from a search that were performed with the Delta M mode set to True. When the Remove Redundant Delta M Hits is set to True, results that nullify a proteoform are removed. For example, if the parameter is set to True and there is an N-terminally acetylated result and a Delta M mode result with Delta M mass (-42) at the N-terminus, the Delta M mode hit will not be shown in the result because it removes a modification which was found through one of the database searches. |
Delta M Mod Tolerance | Defines the tolerance when considering fragments with Delta M modifications. |
Minimum Delta M Fragments | Sets the minimum number of fragments found using Delta M Mode to return a hit. Increase this value to remove false positive Delta M Mode results. The recommended value is 4. |
Calculate FDR | Specifies whether the FDR is calculated. You might see fewer results passing the FDR threshold when 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. |
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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