The Single Proteoform Search node performs proteoform searches against a single proteoform entry. This node also works for data without precursor scans (for example, direct infusion data). To run a search, the application requires a protein sequence and the appropriate modification ID. For more information, see the Perform Single Proteoform searches in the processing workflow. The sequence format is described in the following ProSightPD 4.4 Single Proteoform Search parameters table.
For an example of using this node in a workflow, see Perform Single Proteoform searches in the processing workflow.
The following table lists the parameters for the 4.4 version of the node.
Parameter | Description |
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1. Input Data | |
Proforma sequence | Input a Profroma sequence by inputting the single character abbreviation for each residue. You can add modifications to a residue by putting a modification ID in brackets before the residue to modify. See the Perform Single Proteoform searches in the processing workflow for compatible databases. For example, a human Histone H3 proteoform with its N-terminal methionine removed modified by a K4 methylation and K36 trimethylation is input as: ARTK[AA0076]QTARKSTGGKAPRKQLATKAARKSAPATGGV |
Include N-Term Acetylation | Applies N-term acetylation to the RESID sequence:
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Proteoform Accession | Input an identifier that will appear in the pdResult file. |
Proteoform Description | Input a description that will appear in the pdResult file. |
2. Single Proteoform 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 maximum mass difference for an observed fragment mass to be considered a match to a theoretical fragment mass:
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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. |
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. |
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. |
Include Labile Modification Mass Shift | Target mass will be shifted to account for loss of labile modification mass. |
Labile Modification Mass Shift | Comma separated list of Target mass shifts. |
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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