Database for Searching

Specifies the UniProt XML file containing protein information, such as sequence, accession number, and PTMs.

Run Intact Mass Search

When enabled, specifies the search will match fragment ion masses against theoretical candidate proteoform masses in the database.

Run Fragmentation Search

When enabled, specifies the search will match fragment ion masses against theoretical candidate proteoform masses in the database.

Run Delta M Mode

When enabled, specifies the search will use the mass difference between the theoretical candidate mass and the observed precursor as a potential PTM.

Run Subsequence Search

When enabled, specifies the search will consider smaller subsequences of a proteoform (for example, protein truncation).

Scan Filter Override

Specifies the type of fragmentation to search against.

Precursor Target Tolerance

Specifies the window around the isolated precursor target.

Precursor Tolerance

Specifies the window around the experimental mass from which to pull candidate proteoforms for the fragmentation search.

Subsequence Search Precursor Tolerance

Specifies the window around the experimental mass from which to pull candidate proteoforms for the subsequence search.

Retention Time Tolerance

Specifies the time tolerance for associating fragmentation data with precursors.

Maximum Number of PTMs per Isoform

Specifies the maximum number of PTMs that will be considered for candidate expansion.

Maximum Number of PTMs per Proteoform

Specifies the maximum number of PTMs that will be considered for any single proteoform.

Maximum Number of SNPs per Isoform

Specifies the maximum number of SNPs that will be considered for candidate expansion.

Maximum Mass to Search

Specifies the maximum mass of a protein that will be included in candidate expansion.

Use in Memory Search

When enabled, specifies that all candidate proteoforms will be loaded into memory.

THRASH Window Size

Specifies the isotopic distribution window size.