Re: [Mzmine-devel] How does MZmine identify spectra for library search?

[Pudney Chris (ext) GBJH]

G'day, Sorry, I don't completely understand your question. I will say that the NIST MS Search module makes no changes to the peaks other than to add identification information returned from NIST MS. Regards, Chris. On 24/10/13 23:00, chi zhang wrote: Hi Chris and Tomas, Thanks very much for your reply. It does make sense to the peak lists generated by each sample. But I am still wondering how NIST MS Search works on the peak list after alignment. eg. I used two samples as test to do NIST search with alone and alignment peak lists (3 peak lists). Then I checked a same identification from 3 lists, they all show slightly different spectra peaks. On the other hand, I am still wondering whether the spectra peaks that have been extracted will be took out or returned, whether they can used several times.  Best regards, Chi   2013/10/23 Pudney Chris (ext) GBJH <chris.pud...@syngenta.com> G'day, Yes, I wrote the NIST MS Search module. Regarding you questions: > Does it return all the mass peaks within the RT tolerance then take the top N Max.? From the manual and Help page: https://bit.ly/MZmineManual#h.daszn7p4b0vi "The number of peaks used to form a mass spectrum can be limited by setting the Max. peaks per spectrum parameter to a value greater than zero. If this parameter is set to N then the N rows whose RTs are closest to that of the row (and within the specified RT tolerance) are used to form the mass spectrum." So, it takes the N peaks closest in RT to the peak list row's RT and within the RT tolerance. > And is there any consideration on the deconvolution(there are two or more spectra within the RT tolerance) during this process? No, there isn't. Wouldn't deconvolution be performed separately before searching? Regards, Chris. On 23/10/13 10:12, Tomáš Pluskal wrote: Hi Chi, The NIST search module was written by Chris (in cc), so he might comment on this. But perhaps the best way to find your answers is to read the source code of the module: http://sourceforge.net/p/mzmine/code/HEAD/tree/trunk/src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchTask.java Best regards, Tomas On Oct 22, 2013, at 12:42 AM, chi zhang <zhangch...@gmail.com <mailto:zhangch...@gmail.com>> wrote: Hi guys, I'm trying to process some GC-MS data with MZmine 2 and got some questions about the NIST MS search. Before doing the library search, a spectrum is extracted according to the Spectrum RT tolerance and Max. peaks per sepctrum I set. Anybody could give more details about MZmine how to generate this spectrum? Does it return all the mass peaks within the RT tolerance then take the top N Max.? And is there any consideration on the deconvolution(there are two or more spectra within the RT tolerance) during this process? Thanks to all. Chi ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk_______________________________________________ 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 Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 This 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. This 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.

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