Dear Debojyoti Pal ,

first of all we do not have any idea what software you are talking about. However, I am quite sure that every software has a possiblity to add your own modifications so you can easly edit a iTRAQ modification design to the one you would like to have. Let us know what software you would like to use.

Best,

Michal

Hi Debojyoti Pal ,

As we are not aware of which software you are using, but I hope this will work. But if you want to go for 17,118,119,121 as a 4-plex experiment, then in the search parameter use the Quantitation method as iTRAQ-8plex and discard the remaining labelling details once you get the output. But in such a case, you much repeat the normalization procedure.

Dear Michal Gorka

I am talking about Proteome Discoverer from Thermo. I am not sure how to edit the modification in this software.

Dear Varshasnata Mohanty

The software seems to reject peaks if it doesn't find labelling for all 8 reagents. That is the issue.

Can anyone suggest an alternative software that is known to allow such custom combination of iTRAQ reagents? I can use that software if such functionality exists.

Dear Debojyoti Pal ,

go with MaxQuant. However it is also possible with PD but I guess in MQ it will be easier to set up.

Best,

Michal

Dear Michal Gorka

So I have to acquire data as 8-plex on the regular software (the one that comes with the MS instrument, because it is done at another facility) and THEN analyze the raw data files on MaxQuant, right?

Thanks for your advice

Yes, you just need raw files to run your analysis. I assume that you are using Orbitrap machines to run your samples.

Dear Michal Gorka

Yes, we are using this specifically "Q-Exactive Plus Biopharma-High Resolution Orbitrap" by Thermo. Thank you. I will try your approach and hopefully it would work.

UPDATE: You can also do the same with proteome disoverer. You need to acquire data as usual and then select only relevant labels during analysis.