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Calculate Intensity/Abundance

Hi Guys,

How am I suppose to calculate intensity/abundance? Is it calculated from m/z and retention time? Can someone please help me.

Cheers
plasma33

Re: Calculate Intensity/Abundance

Reply #1
plasma33,

I'm not sure if I understand your question. At what part of xcms are you talking about? The intensity of the peaks for LC-MS data is normally integrated automatically at the start of the process, using the xcmsSet method. There are two different main peak detection algorithms. The first one is good for profile data and older machines, this is the original algorithm which you can read about in the xcms paper (1). The seconded is centWave, which is a high resolution algorithm, citation at below (2).

I suggest having a look at the starting documentation which has an explanation of how xcms works and the ideas behind it. It follows some toy data set but you can of course just drop your own in just as easily. http://www.bioconductor.org/packages/re ... rocess.pdf

Hope it help.

Paul


(1)   Smith, C. A.; Want, E. J.; O'Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787.
(2)   Tautenhahn, R.; Tautenhahn, R.; Böttcher, C.; Böttcher, C.; Neumann, S.; Neumann, S. BMC Bioinformatics 2008, 9, 504.
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: Calculate Intensity/Abundance

Reply #2
Thanks for your reply. I am sorry for being precise. Actually there's no intensity column in the diff report that we get from XCMS. I want to do a compound search in databases such as Metlin, MMCD, HMDB and MassBank but they ask for inputs such as m/z and intensity or retention time and intensity. How am I suppose to calculate intensity from XCMS. Hope I explained it well this time. Waiting for your reply.

Cheers
Vijay

Re: Calculate Intensity/Abundance

Reply #3
plasma33,

So when you get your diffreport you should see that you get something like the following columns:

"mzmed"  "mzmin"  "mzmax"  "rtmed"  "rtmin"  "rtmax"  "npeaks" "KO"    "WT"  "ko15" "ko16" "ko18" "ko19" "ko21" "ko22" "wt15" "wt16" "wt18" "wt19" "wt21" "wt22"

The example above is for the faahKO toy data set. Each file has the intensity values for each feature. So for file ko15 the intensity for 200.1m/z @ 2926s the intensity is 147887.

    mzmed      mzmin      mzmax      rtmed      rtmin      rtmax    npeaks        KO        WT      ko15      ko16
  200.100    200.100    200.100  2926.264  2876.967  2931.740    10.000      5.000      5.000 147887.526 451600.713
      ko18      ko19      ko21      ko22      wt15      wt16      wt18      wt19      wt21      wt22
 65290.385        NA  91635.445 162012.439 175177.079  82619.480        NA  69198.222 153273.469  98144.280

As far as metlin searching goes you should only need the m/z and retention times for the search. If however, you are looking for MS/MS searching (where you'll need the intensity values for searching) you'll need to read and following:
http://www.bioconductor.org/packages/re ... cmsMSn.pdf

hope it's helpful.

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

 

Re: Calculate Intensity/Abundance

Reply #4
Thanks Paul. Really helpful.

Cheers
Plasma33