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. ------------------------------------------------------------------------------ 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=60135991&iu=/4140/ostg.clktrk _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
