Merge pull request #263 from jschrier/my-pages

msconvert instructions

_posts/2023-01-04-Reading-ThermoFischer-XCaliber-RAW-Files.md

@@ -62,4 +62,5 @@ Note that RawTools appears to be a standalone tool with a GUI, so it can probabl
 - (06 Jan 2024) It seems that many packages for working with mass spec in python like [Mass-Suite](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00741-9) and [pyOpenMS](https://github.com/OpenMS/pyopenms-docs) use mzML file formats, not .raw. 
     - [PythoMS](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00055) and [github](https://github.com/larsyunker/PythoMS) seems to support converting from RAW to mzML as well as doing processing, but hasn't been maintained since 2020. Also, [under the hood](https://github.com/larsyunker/PythoMS/blob/master/pythoms/mzml.py) it is just calling  [ProteoWizard](https://proteowizard.sourceforge.io) to call the conversion, and only works under windows
     - [ProteoWizard](https://proteowizard.sourceforge.io) is another recommend tool for converting from RAW to mzML.  [youtube video tutorial](https://www.youtube.com/watch?v=sudY7UtkMQg). But appears to only exist for Windows and maybe Linux.
+        - Specifically the [msconvert](https://proteowizard.sourceforge.io/tools/msconvert.html) tool.
     - [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser) (see also [paper](https://pubmed.ncbi.nlm.nih.gov/31755270/)) is a wrapper around thermo's RawFileReader framework (see section above)