I was reading a paper this morning that I'll need to tell you about later. The paper is really cool, but the tools that are used are cool enough that they deserve their own post.
The tool package in question is the aptly-named ProteomicTools package that you can download from GitHub here. There are an absolute ton of cool features in this interface and the above screenshot is just one tab that you can pull down.
One that looks promising is TurboRaw2MGF. This is a new RAW to mgf or mzml converter with some advanced functionality. While I recommend this conversion is done with the free Proteome Discoverer Viewer software, this isn't going to be applicable to every single workflow. For those of you who need an alternative conversion solution, you might want to check this out.