fix(PD-converter): Enable spectrumFile to be used for run ID in PD converter

[tonywu1999]

Motivation and Context

Similar to this commit, but I'm pretty sure we should use SpectrumFile for the regular MSstats converter. Unit tests for MSstatsPTM seem to assume we use SpectrumFile.

Changes

• Updated clean function to use SpectrumFile for the regular MSstats converter for PD.

Testing

• Unit tests pass in MSstatsConvert, MSstats, MSstatsPTM. Previously, tests in MSstatsPTM were failing.
• Note: I'm a little concerned about backwards compatibility here. People previously using FileID will end up having workflows breaking.
• Future: I'll add a run column for the PD MSstats and TMT converters to enable run ID.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

[mstaniak]

How were people using File.ID? Wasn't Spectrum.File the only working option? If there were actually users who used File.ID, let's add this to news so it's clear that this default changed

[tonywu1999]

@mstaniak

Sorry for the confusion - I read this issue and realized that nobody was using file ID. I'll make a note to update the converters themselves to include a run column