feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format

[tonywu1999]

Motivation and Context

As a part of this issue, we want to add a converter from Metamorpheus to MSstatsPTM format.

Changes

• Added a new MetamorpheusToMSstatsPTMFormat function
• Given there can be multiple modifications on a given peptide in Metamorpheus' output, we will initially set up the converter such that the user targets a specific modification, e.g. "Common Biological:Phosphorylation on S", using the parameter mod_id.
• For now, we will neither remove rows containing a peptide with multiple modifications nor allow users to track multiple modifications (e.g. ProteinId_C_148_S_157). We can always add that feature in the future as an enhancement.

Testing

• Added unit test that verifies that PTM and Protein output are produced with greater than 0 rows.
• Ran R check and generated no new errors or warnings.

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 - requires MSstatsConvert function MetamorpheusToMSstatsFormat to be published to Bioconductor.

[mstaniak]

if ptm_input is data.table, the ptm_input$ part is not needed (so is ", " after it)

[tonywu1999]

I took a look and ptm_input is a data.frame object, so removing the ptm_input$ part results in an error.