Hi Chris, > Sorry, what I'm trying to imply is that if an aligned peak-list has a > set of rows that should clearly be grouped together to form a spectrum > (to pass to NIST MS Search) then there's no guarantee that the values of > PeakListRow.getBestPeak().getRepresentativeScan() for each of the rows > will be identical.
What exactly are you planning to pass to NIST MS search? I can see two ways: 1) Identify the peak list rows that should be grouped together. Then you take their masses [PeakListRow.getAverageMZ()] and intensities [PeakListRow.getAverageHeight()] and you form a "virtual" mass spectrum from these data points. Then you can use this spectrum as a basis for search. In this case, you don't need to touch the actual raw data. 2) Take one representative scan from the raw data and use this scan's spectrum as a basis for search. Of course, you need to choose somehow which scan to use, because PeakListRow.getBestPeak().getRepresentativeScan() will return different scans for different rows. However, does it really matter? How about choosing the first one available? Or choosing the scan with the highest total ion intensity? Tomas =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
