pwilmart/paw_pipeline

A Comet-based, best practices proteomics pipeline.

Proteomics education, tools, and applications

Check out Start_Here for a roadmap to the available content. I have blogs here on some proteomics topics from the simple to the "I can't believe someone wrote a blog post on that". The OHSU proteomics core also has a GitHub account with some additional content.

@[email protected] on Mastodon
@pwilmarth on Twitter

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Phil Wilmarth
July 12, 2020

paw_pipeline's Issues

MSConvertGUI - Raw files are identified as corrupted

Hello Phil,

I started to work with TMT lately for my Master thesis and I'm eager to introduce your well described workflow in our data analysis pipeline. The time you invested in the documentation is tremendous and at this point: Many thanks! I started to follow your workflow but faced the first problem with the MSConverterGUI. The only output I can get is an error message saying my raw files are corrupted, which they are not. I use raw files from a QExactivePlus for TMT2-based quantification and run your scripts with Anaconda 3.6.6. and MSConverter Version 3.0. Are there any incompatibilities or problems you noticed earlier in that context.

Comet Run not Converting SQT Files

Hello Phil,

I am running into trouble running the Comet command. After I hit run, I immediately receive the error as pictured below in my idle console "Warning - folder does not contain any SQT files." How do I remedy this problem? Could it stem from how I set up the program command? Thank you for your help!

Best,
Gabby

Reporter isotopic distribution for TMT

Hi Phil,
I am starting to use PAW pipeline in my TMT studies. The transparency of the workflow and the flexibility is awesome! Although I am not acquainted with Python scripts, I think it is possible to understand what is happening in each step.
However I could not find where to add the correction factors for TMT reporter ions.

Thanks,
Carlo