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CandidateVectorSearch Input Arrays

All findTopCandidates functions require four integer arrays as input:

  • For the CPU versions they are called:
    • candidatesValues
    • candidatesIdx
    • spectraValues
    • spectraIdx
  • For the GPU versions they are called:
    • csrRowoffsets
    • csrColIdx
    • spectraValues
    • spectraIdx

Note that spectraValues and spectraIdx is the same for both versions. The following should highlight how to get these arrays.

Consider two peptides with the following ion m/z values:

peptide_1 = [321.3251, 531.7851, 556.2134, 643.9867, 989.9911]
peptide_2 = [301.4156, 411.6598, 713.7981, 754.3412, 811.9812, 871.4351]

And the following two spectra with m/z values as given:

spectrum_1 = [135.7413, 321.3251, 531.7851, 989.9911]
spectrum_2 = [101.8931, 301.4156, 713.7981, 754.3412, 811.9812, 871.4351]

candidatesValues and csrColIdx

The candidatesValues and csrColIdx array are the same. They contain all ion m/z values from all peptides concatenated. The values should be multiplied by 100 and rounded to the nearest integer. Note that CandidateVectorSearch only supports m/z values up to 5000 so anything beyond that should be discarded!

candidatesValues = [32133, 53179, 55621, 64399, 98999,
                    30142, 41166, 71380, 75434, 81198, 87144]
csrColIdx = candidatesValues

candidatesIdx

The candidatesIdx array indicates the starting position of every peptide in candidatesValues. It always contains as many elements as there are peptides!

candidatesIdx = [0, 5]

csrRowoffsets

Analogous to candidatesIdx the array csrRowoffsets indicates start and end positions of all peptides in the csrColIdx array. This follows the CSR format as described here. The csrRowoffsets array always contains number of peptides + 1 elements!

csrRowoffsets = [0, 5, 11]

spectraValues

The spectraValues array contains all m/z values of all peaks of all spectra. Again the values should be multiplied by 100 and rounded to the nearest integer. Peaks with m/z values greater than 5000 should be discarded!

spectraValues = [13574, 32133, 53179, 98999,
                 10189, 30142, 71380, 75434, 81198, 87144]

spectraIdx

The spectraIdx array is analogous to the candidatesIdx array and contains the indices of where each spectrum starts in spectraValues. It always contains as many elements as there are spectra.

spectraIdx = [0, 4]

Code example

A code example where functions are called from a C# application is given in here (CPU) and here (GPU).