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 ------------------------------------------------------------------------------ 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
