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.

Table ProSightPD 4.4 Single Proteoform Search parameters

Parameter

Description

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
K[AA0074]KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Include N-Term Acetylation

Applies N-term acetylation to the RESID sequence:

  • True
  • False

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:

  • Minimum value = 1 ppm
  • Maximum value = 2 Da |50 ppm

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:

  • High—The total number of CPU cores less 1
  • Medium—Half the number of available cores
  • Low—1 core

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:

  • 4—recommended for maximizing IDs
  • 9—recommended for maximizing characterization