kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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How to go on? #25

Closed sorenwacker closed 5 years ago

sorenwacker commented 5 years ago

I wonder what would be a suggested downstream analysis toolchain after processing the raw files with RawTools. Apparently, the tool generates the chromatogram and the matrix.txt as well as the peaklist mfg files. But how would you continue from here to assembled peptides and proteins? Any advise, recommendation?

chrishuges commented 5 years ago

This is really going to be up to you as you have many options here. RawTools will give you different outputs depending on how you have used it. Some of the files are useful for quality control and method development purposes (such as the parse files, or those generated with the actual QC function). Others are useful for visualizing your data (chromatogram files). Others are useful for getting quantification values (matrix.txt files). RawTools will also perform searches of your data (using X!Tandem or IdentiPy) as discussed on the wiki pages. These searches are good for generating quick insights into your data (labeling efficiency, digestion efficiency, etc...).

But, it appears you are interested in getting a complete and validated protein and peptide list from your entire data set. In this case, you will want the MGF output generated by RawTools. From here, you can search this MGF output with any proteomics search engine that will take this as input (most tools will). I personally like the SearchGUI and PeptideShaker tools developed by the Compomics group. There are great walkthroughs on their respective pages for searching and validating your peptide and protein data. If you want quantification information, simply combine the matrix.txt output from RawTools with the peptide report generated by PeptideShaker.

But, these are by no means your only option. As I mention above, most search tools will take an MGF as an input for a search to generate your peptide and protein lists.

sorenwacker commented 5 years ago

Thanks for your advice. We will check out these routes. Your commends are much appreciated!