Hi Joachim, > > thank you for your reply. Are really all the different m/z values in this > plot (from 14.50 – 18.00 min) used for calculation of the median ?
Yes. > > We found no way to improve the m/z assignment using any of the parameters > available in the chromatogram builder. > m/z tolerance had no influence at all which seems to be strange. One problem is that you are looking at the whole chromatogram. You will see the value improve if you run the peak deconvolution, because then the m/z value will be calculated again for individual peaks resolved from the chromatogram. > > 533.1737 is the centroided m/z. Setting m/z tolerance to 0.001 should limit > the mass range used for the calculation of the mass chromatogram to > 533.1727-533.1747. MZmine does not know the term "centroided m/z". MZmine looks at the individual m/z values detected in each scan. > The picture you send includes an m/z range from 533.1695 – 533.1748. Thus we > asking ourselves where the give m/z tolerance is actually used. Could you > please check if this feature was correctly implemented or give us an > explanation how the m/z tolerance is applied. The m/z tolerance is used in the following way: if the last point of the chromatogram is X m/z, then the following point must be X +- m/z tolerance. If the following point falls within this tolerance range, it will be connected to the same chromatogram. Therefore, theoretically it might happen that in consecutive scans you would have values such as scan 1: 500.001 m/z scan 2: 500.002 m/z scan 3: 500.003 m/z scan 4: 500.004 m/z scan 5: 500.005 m/z etc. These all would be connected to the same chromatogram with m/z tolerance = 0.001, because the mass difference between individual consecutive scans is <= 0.001 m/z. > From our point of view the settings of the m/z tolerance should already > limit the generation of the mass chromatograms to the m/z values found during > mass detection. Later changes by calculation of median may significantly > influence the accurate m/z and usage of the wrong m/z then leads to > misinterpretation. Actually, the reason to use median is to improve the mass accuracy, compared to simply using the m/z value of the highest data point. But you need to run peak deconvolution to make sure the median values are calculated from the proper regions of the retention time. Best, Tomas =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Mzmine-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mzmine-devel
