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Handle Proteome Discoverer scores #5

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524D opened this issue May 22, 2024 · 0 comments
Open

Handle Proteome Discoverer scores #5

524D opened this issue May 22, 2024 · 0 comments
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enhancement New feature or request

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@524D
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524D commented May 22, 2024

It would be nice if mzRecal could use mzid data produced by Proteome Discoverer, since many datasets in PRIDE contain search results in that format. However, the PD score reporting is in a non-standard userParam tag, where the meaning of score value is unknown. E.g.

        <SpectrumIdentificationResult spectraData_ref="XXX" spectrumID="scan=1234 file=678" id="SIR_1234_678">
          <SpectrumIdentificationItem passThreshold="true" rank="1" peptide_ref="-9876_56432_00000" experimentalMassToCharge="666.666" calculatedMassToCharge="666.777" chargeState="3" id="SII__1234_44444_1">
            <PeptideEvidenceRef peptideEvidence_ref="PE_44444_-1111" />
            <userParam name="Proteome Discoverer Delta Score" value="0.7070" />
          </SpectrumIdentificationItem>
          <cvParam accession="MS:1000894" cvRef="PSI-MS" name="retention time" value="99.9999" />
        </SpectrumIdentificationResult>

@524D 524D added the enhancement New feature or request label May 22, 2024
@524D 524D self-assigned this May 22, 2024
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