Hi Steve, You may consider checking other software packages that use mzML. If you find any discrepancies between the CV terms used, let me know so we can fix it in MZmine as well.
Best regards, Tomas On Aug 31, 2011, at 10:15 PM, Robles, Steve wrote: > Tomas, > > I thought if the software was displaying the value as retention time then it > was probably coming from a term with "retention time" either in its name or > description. The mzML elution time term has a different meaning but in > general elution time and retention time usually refer to the same thing. > > I'm not really familiar with mzML common practice. I'm going by the schema > documentation and a few examples. Basically we started off just supplying the > mandatory elements and terms, and then threw in a couple of extra. > > Thanks for the fast reply, > > > Steven Robles > Design Engineer - Software > LECO Corporation - Separation Sciences > http://www.leco.com > > > > -----Original Message----- > From: Tomas Pluskal [mailto:plus...@oist.jp] > Sent: Wednesday, August 31, 2011 3:17 AM > To: Developer discussion > Cc: Robles, Steve > Subject: Re: [Mzmine-devel] reading retention time from mzML > > Hi Steve, > > As far as I understand, the common practice in mzML is to use the term > MS:1000016 for retention time: > > [Term] > relationship: has_units UO:0000031 ! minute > id: MS:1000016 > name: scan start time > def: "The time that an analyzer started a scan, relative to the start of the > MS run." [PSI:MS] > xref: value-type:xsd\:float "The allowed value-type for this CV term." > is_a: MS:1000503 ! scan attribute > relationship: has_units UO:0000010 ! second > > > That is also what we expect in MZmine. > > What is the basis of your decision to use MS:1000895 or MS:1000826? > > Best regards, > > Tomas > > > On Aug 31, 2011, at 5:09 AM, Robles, Steve wrote: > >> Hello, >> >> Our software exports mzML 1.1 and the most recent version of MZmine 2.2 can >> open the files but it doesn't seem to read the retention time. >> >> The specific mzML includes local retention time and elution time CV elements >> but these don't show up. See terms below and attached mzML for an example. >> Can anyone give me an idea what we need to include in our mzML so MZmine >> will display the retention time? >> >> I hope I'm sending this to the write place and apologize if I'm not. >> >> Thank you, >> >> Steven Robles >> Design Engineer - Software >> LECO Corporation - Separation Sciences http://www.leco.com >> >> >> >> >> [Term] >> id: MS:1000895 >> name: local retention time >> def: "A measure of the interval relative to the beginning of a mass >> spectrometric run when a peptide will exit an unspecified local >> chromatographic column and instrumental setup." [PSI:MS] >> xref: value-type:xsd\:float "The allowed value-type for this CV term." >> is_a: MS:1000894 ! retention time >> relationship: has_units UO:0000010 ! second >> relationship: has_units UO:0000031 ! minute >> >> [Term] >> id: MS:1000826 >> name: elution time >> def: "The time of elution from a chromatographic column, relative to >> the start of the chromatography." [PSI:MS] >> xref: value-type:xsd\:float "The allowed value-type for this CV term." >> is_a: MS:1000503 ! scan attribute >> relationship: has_units UO:0000010 ! second >> relationship: has_units UO:0000031 ! minute >> >> LECO Corporation Notice: This communication may contain confidential >> information intended for the named recipient(s) only. If you received this >> by mistake, please destroy it and notify us of the error. Thank you. >> >> <25 DST+PFTBA Stick 25sps >> CA0.5_4_PEAKS.mzML>--------------------------------------------------- >> --------------------------- Special Offer -- Download ArcSight Logger >> for FREE! >> Finally, a world-class log management solution at an even better >> price-free! And you'll get a free "Love Thy Logs" t-shirt when you >> download Logger. Secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsisghtdev2dev__________________________________ >> _____________ >> 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 > > > > > ________________________________ > > LECO Corporation Notice: This communication may contain confidential > information intended for the named recipient(s) only. If you received this by > mistake, please destroy it and notify us of the error. Thank you. > > ------------------------------------------------------------------------------ > Special Offer -- Download ArcSight Logger for FREE! > Finally, a world-class log management solution at an even better > price-free! And you'll get a free "Love Thy Logs" t-shirt when you > download Logger. Secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsisghtdev2dev > _______________________________________________ > 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 ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
