Help with XCMS parameters

August 12, 2011, 08:26:35 AM

Hello,

I am new to the XCMS software and I am using the online version. I am trying to optimize the parameters and need help. I have my samples run in LC-MS (API3200 triple quad in MS1 mode using Q1 scan) with a resolution of 0.1 amu, and scan speed of 0.7700 sec (including pause). the run time is 60 minutes (period 1- 40 minutes, period 2- 20 minutes). I convert the .wiff files into .mzxml files using the following command prompt:

"mzwiff -v -c1 -s1 --mzXML filename"

From the raw data, the peaks are narrow with a FWHM of ~10 and retention time deviation of 0.2 minutes.

I use the following parameters:

Feature detection: matched filter method: FWHM-10, step size- 0.1, S/N cutoff 15, mzdiff 0.5, retention time correction: obiwarp method: step size-0.1, alignment: mzdiff- 0.75, minfrac- 0.5, bw- 15.

What is the best way to analyze this data. Any suggestions would be greatly appreciated.

Thank you

Prashanthi

Re: Help with XCMS parameters

Reply #1 – August 12, 2011, 11:02:17 AM

The "HPLC / Single Quad MS" parameter set should give you a good base line for parameter optimization.