Exporting integrated peak lists for every m/z value in LCMS
Posted: Wed Apr 12, 2006 8:39 am
Hello,
This is two questions really:
1) I routinely run complex plant extracts on LCMS and want to integrate all peaks found at every m/z value with unit mass resolution, then export this list to a text file or similar. For example, if I scan in the range of 100-400 m/z, I would like a list of 300 m/z values over the range 100, 101, 102...400 in rows, and then in columns a retention time header, with integrated peak areas filling the matrix. At the moment we gather data using Xcalibur, and none of the Xcalibur quantification functions can produce this sort of data. I have experimented with the xcms program developed at Scripps; this runs on R using .mzXML data files and is quite good at peak-picking and also retention time correction in the fashion described, but is not so good at peak integration. Any suggestions as to how I can do what I want with Xcalibur .raw files?
2) If I have an a priori starting list of retention time and m/z values for a plant extract , this often runs into the hundreds of components. In Xcalibur, in order to set up a quantification method, each peak has to be entered manually. There is no facility to import a list of retention time-m/z pairs. Does anyone know how this can be done, either with Xcalibur, or with 3rd party integration software that can read Xcalibur .raw files, or alternatively .cdf or .mzXML files?
thanks
Tony
This is two questions really:
1) I routinely run complex plant extracts on LCMS and want to integrate all peaks found at every m/z value with unit mass resolution, then export this list to a text file or similar. For example, if I scan in the range of 100-400 m/z, I would like a list of 300 m/z values over the range 100, 101, 102...400 in rows, and then in columns a retention time header, with integrated peak areas filling the matrix. At the moment we gather data using Xcalibur, and none of the Xcalibur quantification functions can produce this sort of data. I have experimented with the xcms program developed at Scripps; this runs on R using .mzXML data files and is quite good at peak-picking and also retention time correction in the fashion described, but is not so good at peak integration. Any suggestions as to how I can do what I want with Xcalibur .raw files?
2) If I have an a priori starting list of retention time and m/z values for a plant extract , this often runs into the hundreds of components. In Xcalibur, in order to set up a quantification method, each peak has to be entered manually. There is no facility to import a list of retention time-m/z pairs. Does anyone know how this can be done, either with Xcalibur, or with 3rd party integration software that can read Xcalibur .raw files, or alternatively .cdf or .mzXML files?
thanks
Tony