Hi Chris, > As far as I understood, I suppose your data is GC-MS and so you use MS scans > and compare them to the NIST library.
Yes, that's correct. > Perhaps we can assume that the spectra of aligned peaks should be similar, as > long as the alignment is correct. > Therefore I would suggest to use > PeakListRow.getBestPeak().getRepresentativeScan() as a basis for NIST search. I had initially considered this. The same approach can be applied to peak-lists from a single raw data file. However, I rejected it for the following reason: Suppose you have an aligned peak-list and have (manually) identified a set of peak-list rows that are part of the same spectrum. There's no guarantee (in fact it's quite likely?) the peak-list rows will all return identical values for PeakListRow.getBestPeak().getRepresentativeScan(). This is because for each of the peak-list rows, getBestPeak() could be any one of the row's aligned peaks, each of which will return different values for getRepresentativeScan(). Does that make sense? 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
