G'day, > What exactly are you planning to pass to NIST MS search?
I'm passing the list of (m/z, intensity) pairs, one pair for each of the peak-list rows that I've grouped together. > 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? For aligned peak-lists, whether the m/z and intensity values are the average or "best" of each row isn't so much the issue as how to group the rows in the first place. I think I'll stick with what I've got for the moment, i.e. make multiple passes through the aligned peak-list, processing a different raw data file on each pass. Thanks, Chris. Syngenta Limited, Registered in England No 2710846 Registered Office : Syngenta Limited, European Regional Centre, Priestley Road, Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ 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
