Does anyone know of a good resource for mass spec analysis workflow?

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Saravanan Kumar Popular answer

Hi Samantha,

Go through the Trans-proteomic Pipeline, its an open source software pipeline for the analysis of mass spec data-sets. I have mentioned the link for the website and tutorial.

You may consider using MaxQuant - open source tool for LFQ of Proteome datasets.

All the Best for your efforts.

http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial_v1

http://www.coxdocs.org/doku.php?id=maxquant:start

Article A Guided Tour of the Trans-Proteomic Pipeline

Article The MaxQuant computational platform for mass spectrometry-ba...

Alexis Delabriere

Hello,

Could you precise if your data are proteomics, metabolomics or others ? As you got .raw I assume that you work with a thermo of high resolution. The processing is really different depending of your data type.

Moreover could you precise if it's LC-MS, GC-MS or other ?

If it is metabolomics, I'll try to help a little.

Saravanan Kumar

Samantha Jeschonek

This seems like exactly what I was looking for! Thanks for the pipeline paper!

Luke V Schneider

It all starts with getting the most out of your raw data.

Poster Improved MS/MS Peptide Identification Using Advanced Peak De...

Method Mass Spectral Data Processing

Kristian E Swearingen

I also recommend the Trans-Proteomic Pipeline (TPP) for ease of use, quality of documentation, and quality of support from the user community and the developers. The TPP comes with the Comet search engine (the direct descendant of SEQUEST by Jimmy Eng), which is as good as any out there and is very fast, even on a stand-alone PC. You can convert your .raw files to .mzML right in the pipeline - the TPP incorporates MsConvert from Proteowizard. However, depending on whether you have the necessary MS vendor files on your PC, you might have better luck just downloading the Proteowizard package and running mscovert as a stand-alone. For label-free quantification, you can manually do it fairly easy by spectral counting (I prefer the Normalized Spectral Abundance Factor approach, Zybailov 2006). You can also use a slighly more sophisticated approach, the Normalized Spectral Index, which is inlcuded in the St.Peter tool in the TPP.

http://proteowizard.sourceforge.net/

https://www.ncbi.nlm.nih.gov/pubmed/16944946

Thanks again! These are wonderful resources!

Syed Azmal Ali

HI Samantha,

You have already got wonderful support in the form of comment related to TPP. Additionally, I like to advise you to use multiple search engines in the TPP spectra searching (COMET, TANDEM, and SpectraST). Combine them all with iProphet (an integral part of TPP), you will get much better identification and confidence than using the single search engine. And then go for label free approach.

Best of Luck

Michael Shortreed

MetaMorpheus(https://github.com/smith-chem-wisc/MetaMorpheus) is a new open source graphical user interface that works in Windows and Linux environments for the identification of peptides in bottom-up data. With it you can discover unknown post-translational modifications, calibrate your spectra and quantify your peptides. It's fast and easy to use.