Intensity values ??minimally reliable

January 10, 2013, 06:45:33 AM

Hi,

I've been processing UPLC/Q-TOF according with

http://www.nature.com/nprot/journal/v7/ ... 54_T1.html

and then with CAMERA standard workflow. I finish with proposed mass peaks that seem reasonable, for example, for plants they match kegg's secondary metabolism, Porphyrin and chlorophyll metabolism, and so on. But when I look to peak intensities they are very low, some less than 1000. If a peak pass all filters, matching all samples, in my case 30 samples, can I trust it can be a real peak or not?

Looking at this table http://mzmatch.sourceforge.net/metabolo ... isobar.tsv

from a serial dilution there are peak intensity as low as 4000, from filtered peaks, can it be a possibility that in my case I have a problem of concentration?

thanks in advance...

Re: Intensity values ??minimally reliable

Reply #1 – January 10, 2013, 01:32:08 PM

A "trustworthy" intensity threshold really depends on your instrument. If the EIC looks OK then you can trust it to be a real peak.

But at the end of the day you want to be able to acquire MS/MS data on an "interesting" feature, and you need to find out what the minimum intensity is for that on your instrument.
The threshold that you choose will most likely be a function of the metabolite mass and also depend on the isolation window (,i.e. - efficiency ...).