feat(protein-prospector): Add TMT converter for protein prospector

[tonywu1999]

Motivation and Context

In this issue, one of our users is requesting a new PTM+TMT converter for Protein Prospector. In order to create this converter, we first need to create a TMT converter.

Changes

• Add a new internal function .cleanRawProteinProspector to clean up the protein prospector output
• Create new ProteinProspectortoMSstatsTMTFormat function with basic functionality

Testing

• Examples from .Rd files run successfully
• Locally tested on a 45MB dataset and it processed successfully.
• Added unit tests

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

[tonywu1999]

TODO:

• Determine how to handle 0s, negative values, and values between 0 and 1
• Add unit tests on 0-1, 0s, & negative value handling

[mstaniak]

Hi @tonywu1999 , adding 1:n() to PSM is meant to help retain the identity of PSMs when melting, right?
The single underscore will/might be a problem for dataProcess(), "_[PSM ID]" should be removed after aggregating PSMs.
Also the := will work a bit better, data.table might have a faster ifelse, too

[tonywu1999]

@mstaniak

adding 1:n() to PSM is meant to help retain the identity of PSMs when melting, right?

Yes, and I believe retaining the identity of PSMs is needed when aggregating them here within the same run/sequence/charge combination.

The single underscore will/might be a problem for dataProcess(), "_[PSM ID]" should be removed after aggregating PSMs.

It looks like the single underscore from adding 1:n is removed here.

Also the := will work a bit better, data.table might have a faster ifelse, too

I ended up updating the code to use := when adding the PSM column

addressed feedback