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
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 (http://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.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.
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
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 (http://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcmsMSn.pdf)
hope it's helpful.
Paul
Thanks Paul. Really helpful.
Cheers
Plasma33