Hi Chris, I am not sure I understand correctly your approach. Is your data coming from GC-MS or LC-MS? Are you searching MS scans or MS/MS scans?
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. 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. How about that? Tomas On Jan 20, 2011, at 3:45 PM, Pudney Chris (ext) GBJH wrote: > G'day, > > I'm working on a module that uses the NIST MS Search program > <http://chemdata.nist.gov/mass-spc/ms-search/> to identify peaks. > > NIST MS Search takes spectra as input for its searches. Each spectrum > is defined by a set of one or more (mass, intensity) pairs. > > Given a peak-list in MZmine 2 I generate search spectra by grouping > together peaks that have identical scan-numbers (as given by > ChromatographicPeak.getRepresentativeScanNumber()). > > This works well for peak-lists with a single peak per row, i.e. > peak-lists that correspond to a single raw data file. However, for > peak-lists with *multiple* peaks per row, e.g. aligned peak-lists, > things become more difficult. > > I was wondering how to extract spectra from such peak-lists. The > scan-number method no longer works as each row has multiple scan-numbers > (one per peak). > > The approach I've taken is to treat these peak-lists as several > individual peak-lists, one for each of the raw data files it has. Then > I run the search for each of these individual peak-lists, combining > their search results in the original peak-list. This works but I'm a > little concerned that any information gained by alignment of the > peak-lists isn't being taken advantage of. > > I'd be grateful for any suggestions or comments? > > I hope to commit this module to the project repository in the coming weeks. > > 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. > > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > =============================================== 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 ------------------------------------------------------------------------------ Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
