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ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
https://protprotocols.github.io
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Add support for RawTools? #93

Open chrishuges opened 5 years ago

chrishuges commented 5 years ago

Has your group considered adding support for RawTools? This would give a few benefits:

  1. You could use it to make your MGF inputs in an operating system independent manner (e.g. Windows, MacOS, Linux).
  2. You can use it to get your isobaric tag quantification values out.
  3. You can use it to get precursor area values out.

RawTools currently only requires .NET (Mono on MacOS and Linux - although the newest RawFileReader now supports .NET Core 2.0, so Mono might not be required for much longer) and is open source. Although, the ThermoRawFileParser from compomics (for converting raw files to MGF) might be a bit easier for you integrate since you are already in that ecosystem with SearchCLI and PeptideShakerCLI. Just a thought.

veitveit commented 5 years ago

@chrishuges This is definitely worth considering. We are planning to add the ThermoRawFileParser. If the conversion is covered by RawTools, we could add some QC measures for the raw files as this part is missing.

@jgriss any thoughts?

jgriss commented 5 years ago

Yasset together with compomics created a Java wrapper for this that should be straight forward to integrate (covering the conversion bit): https://github.com/ypriverol/ThermoRawFileParser

But since the project also has some kind of R bindings, I'm quite sure that we can use all their features in our notebook