search

compomics / reporter

Protein quantification based on reporter ions
http://compomics.github.io/projects/reporter.html
4 stars 2 forks source link

raw/corrected TMT intensities with reporter #9

Closed korbini closed 5 years ago

korbini commented 5 years ago

Hi, is it possible to export raw/corrected TMT intensities with reporter? I haven't seen an option for this. It would be nice for further processing with e.g. limma.

hbarsnes commented 5 years ago

Hi,

Yes, this is support both via Export > Quantification Features in the graphical user interface or via the command line. For the command line option, please see this recent discussion: https://github.com/compomics/reporter/issues/8.

Best regards, Harald

korbini commented 5 years ago

Hi thank you for your quick response. If I am not mistaken reporter only exports ratios and not intensities. - Or maybe I have missed something. This would be also nice to know regarding the signal-to-noise ratio.

hbarsnes commented 5 years ago

If I am not mistaken reporter only exports ratios and not intensities

If you don't select a reference sample you should get just the intensities. I think. :)

korbini commented 5 years ago

Looks like ratios to me (also says in row above) :(

hbarsnes commented 5 years ago

Not sure how it can be ratios when there is nothing to divide them on? (i.e. no reference sample)

korbini commented 5 years ago

These one digit values look like ratios IMHO (example attached). Could it be ratios to median/mean? I would be interested in the raw TMT signal intensity.

AGLGSPERPPK.pdf AGLGSPERPPK.xlsx

hbarsnes commented 5 years ago

Yes, you are correct. The intensities are by default normalized relative to the median for the peptides and the proteins, but not for the PSMs.

You can control this via the graphical user interface via the Advanced Settings at the bottom of the New Project dialog. Click the Edit button next to the Quantification field and then select normalization. There you can choose the normalization option for each level, or turn it off.

From the command line see the options normalization_psm, normalization_peptide and normalization_protein.

korbini commented 5 years ago

Thank you! Forgot about these.

sorenwacker commented 5 years ago

Is there are place where the normalization is formally written down anywhere?

mvaudel commented 5 years ago

I am afraid there is currently no detailed documentation on this. We are working on a major update of our code, we will update the documentation after this.