Hello,

Our lab is working on search software that extends Morpheus, called MetaMorpheus ( https://github.com/smith-chem-wisc/MetaMorpheus ). One format that we output is mzIdentML, which I would like to be able to import into Skyline. However, only some scoring mechanisms are supported by Skyline; we have a q-value output that we would like to use. MS-GF outputs q-values and these are supported by Skyline, so it should not be much of a stretch to import our q-values. We don't have CV terms yet, but would it be possible for Skyline to support a generic q-value (already listed by PSI-MS)?

[Term]
id: MS:1002354
name: PSM-level q-value
def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002347 ! PSM-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

An example mzML and mzID from MetaMorpheus (yeast lysate) can be found at:
https://uwmadison.box.com/s/6uaasr4foe3vf5eyjz4mko3wjy3x6iog

If you simply find+replace the following, Skyline will import correctly, otherwise it will give an unsupported score error upon import:

'accession="MS:1002354"' replace with 'accession="MS:1002054"'
'name="PSM-level q-value"' replace with 'name="MS-GF:QValue"'

Thank you for your time,
Rob Millikin
UW-Madison