H/L ratio setting in dimethyl labeling is missing

[Sameh Magdeldin]

Dears

I'm trying to process dimethyl labeling data in peptide shaker. After successful setting the parameters as recommended, the final report cames up with dimethylated peptides. 

I could not find the way to set the relative quantification . for example heavy/ light ratio. is there any way to get the relative quant?

thanks 

[Marc Vaudel]

Hi,

Thank you for your interest in PeptideShaker. The tool solely processes identification results and cannot do relative/absolute quant. If you want to do quantification we recommend using a dedicated tool like MaxQuant.

Hope this helps,

Marc

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[Sameh Magdeldin]

Thanks a lot for your reply. i guess this is an important feature that needs consideration in future in possible

regards

[Antonio Ortega]

Dear Sameh.

I faced a similar problem, performing quantification on label-free DDA data, a few months ago.

In my case, I got my quantification done without MaxQuant by doing the following:

- Passing the peptide shaker Default PSM (Peptide to Spectrum Matches) reports in txt format to moFF https://github.com/compomics/moFF

As I understand it, this program is capable of running (I) MBR (Match Between Runs), to increase the number of identified spectra and (II) Apex Intensity extraction to preprocess MS1 intensity signals and make them consistent. More info is available on the Protocol Exchange paper here https://www.nature.com/protocolexchange/protocols/5233

- Passing moFF output to MSqRob, an R package that performs relative quantification by implementing a robust ridge regression model https://github.com/statOmics/MSqRob. More info on any of the published papers for this program, for example: https://www.sciencedirect.com/science/article/pii/S1874391917301239

In theory moFF is not essential, but it's very useful because it boosts your identifications (i.e decreases missing data) and makes intensity measurements more consistent across runs.

What you get in the end is a table where every row is a protein. Fields include fold change and signficance of the difference. I put it all together in a GitHub repo, but unfortunately it is still not tested nor well documented https://github.com/antortjim/Thesis-Code/tree/master/pipeline

These tools were not developed by me. moFF was made at the Compomics group at University of Ghent and MSqRob at the statOmics group also at UGhent.

Hope it helps,

Antonio