XCMS has a limit of 9999 scans?

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XCMS has a limit of 9999 scans?

June 17, 2013, 06:23:05 PM

Recently, I meet a problem that XCMS only can identify the peaks of GC/MS (single quadpole) with biggest number of scans 9999 !
Do anyone find this limitation ?
Who can tell me how to resolve this problem? Thanks.

Re: XCMS has a limit of 9999 scans?

Reply #1 – June 18, 2013, 04:39:26 AM

Hi,

can you give a more specific example ? A code snippet ? Possibly example data ?
What is "identify" ? Do you mean clicking into a plotChrom(ident=TRUE) ?

Yours,
Steffen

Re: XCMS has a limit of 9999 scans?

Reply #2 – June 22, 2013, 03:38:54 AM

Hi, Steffen,
My question was explained as follows,
I use Agilent 7890A/5975C GC/MS (Single Quadpole) with full scan mode of 5 specta/second to acquire metabolomics data. The data acquirement time is 43 min (excluding solvent delay time), which is 12900 scans. But the export file of XCMS only displayed the results of 9999 scans. I attempted XCMS and onlineXCMS and the results are the same.
I think I should send ".CDF" format files to you, could you PM your email box to me? Thanks!

Yours,
Xianfu

Re: XCMS has a limit of 9999 scans?

Reply #3 – June 24, 2013, 03:20:41 AM

I make a mistake!
Prior to being analyzed by XCMS, I usually tranformed the raw files to nominal CDF format files by Metalign. The default value of Retention range is 1-10000 scans. When scan speed of MS was increased, the retention range should be paid attention. I have corrected this mistake when again tranforming raw data to nominal CDF format files, and the xcms output is OK.
So XCMS doesn't limit scan numbers.

Re: XCMS has a limit of 9999 scans?

Reply #4 – June 24, 2013, 01:18:49 PM

Hi,

if you want to limit an xcmsSet to a certain (RT) range you can specify the scanrange=c(min,max) parameter,
where min and max are scan numbers (and not RT in minutes or seconds), so that depends
on the scan frequency.

Yours,
Steffen