From: Eric D. <Eri...@sy...> - 2013-09-04 20:11:54
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Hi Brian, I agree, this is an improvement. I tweaked the language a little so all the definitions are in the same tense and added a “from”. How does everyone like these improved definitions? id: MS:1000894 name: retention time def: "A time interval from the start of chromatography when a peptide exits a chromatographic column." [PSI:MS] id: MS:1000895 name: local retention time def: "A time interval from the start of chromatography when a peptide exits an unspecified local chromatographic column and instrumental setup." [PSI:MS] id: MS:1000896 name: normalized retention time def: "A time interval from the start of chromatography when a peptide exits a standardized reference chromatographic column and instrumental setup." [PSI:MS] id: MS:1000897 name: predicted retention time def: "A time interval from the start of chromatography when a peptide exits a chromatographic column as predicted by a referenced software application." [PSI:MS] *From:* Brian Pratt [mailto:bri...@in...] *Sent:* Wednesday, September 04, 2013 11:50 AM *To:* Eric Deutsch *Cc:* Mass spectrometry standard development; psi...@li...; psi...@li... *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo It's the "relative to the beginning of a mass spectrometric run" part that strikes me as misleading - it doesn't seem proper when the chromatography may have taken place in a completely different time period than the mass spec analysis (again, thinking MALDI but trying to be perfectly general and futureproof). It just seems inline-LCMS-centric where it should be more general. Overall I would think it should use language about the column's history rather than the mass analyzer's. So for example id: MS:1000897 name: predicted retention time should simply read: def: "A time interval when a peptide will exit a chromatographic column as predicted by a referenced software application." [PSI:MS] and id: MS:1000894 name: retention time should be def: "A time interval at which a peptide exited a chromatographic column." [PSI:MS] etc. Perhaps I am revisiting an already settled issue, but this just isn't intuitive to me as currently written. And I might just be the target audience, as a developer dipping into this on an occasional basis. Helpfully, Brian Pratt On Wed, Sep 4, 2013 at 10:12 AM, Eric Deutsch < Eri...@sy...> wrote: Hi Brian, can you elaborate on what is misleading? I don’t see how concurrent elution and scan are implied in these terms? Maybe the term “mass spectrometric run” is the vague part? Perhaps “chromatography” should replace “a mass spectrometric run” for terms 894-896? For pepXML, you almost surely want “scan start time” since that’s what is pulled from the raw/mzML files, right? The true retention time of the peptide ion seen in that scan is far more complex and usually not known very well. The scan start time is a precise and often sufficiently useful proxy for the true retention time. Right? Allowed units are specified in the term metadata, see below.. Eric 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 is_a: MS:1001105 ! peptide result details is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute id: MS:1000894 name: retention time def: "A measure of the interval relative to the beginning of a mass spectrometric run." [PSI:MS] is_a: MS:1000887 ! peptide attribute 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 id: MS:1000896 name: normalized retention time def: "A measure of the interval relative to the beginning of a mass spectrometric run when a peptide will exit a standardized reference 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 id: MS:1000897 name: predicted retention time def: "A time interval relative to the beginning of a mass spectrometric run when a peptide will exit a chromatographic column as predicted by a referenced software application." [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 *From:* Brian Pratt [mailto:bri...@in...] *Sent:* Wednesday, September 04, 2013 9:56 AM *To:* Mass spectrometry standard development *Cc:* psi...@li...; psi...@li...; Eric Deutsch *Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] New version 3.50.0 of psi-ms.obo >> What do you think? I completely agree that these are distinct concepts, and of course I'm not surprised that everyone else thinks so too. But the description is misleading, I think, since it really seems to assume concurrent elution and scan. A quibble perhaps but probably worth cleaning up. The use in question is actually in pepXML related code, so retention time is the concept we want for sure. But now I guess I have to think about managing units? Or is it defined as being in seconds? (And if so, perhaps the description should be enhanced to reflect that?) Thanks, Brian On Wed, Sep 4, 2013 at 9:45 AM, <Eri...@sy...> wrote: Hi Brian, I'm not certain if that answers your question, but I might add that ProteoWizard's use of the obsolete retention time(s) should be changed to either scan start time or retention time. We intend scan start time to be used in cases where there is a time tag associated with a definite mass spec acquisition (as is the case in mzML and mzIdentML). The non-obsolete retention time term should be used as an attribute associated with a peptide molecule in a chromatographic column independent of an instrument acquisition event (as is the case in TraML). The MALDI case is a little more tricky. In practice, a scan start time will likely be recorded with the instrument and should be written into mzML et al. The chromatographic retention time might be known and could be recorded separately (as this will be a different time than the instrument scan time), but often is not well known when the mzML is written. But as you allude to, these are now different concepts with different terms, whereas before it was more muddled. What do you think? Regards, Eric > -----Original Message----- > From: Gerhard Mayer [mailto:Ger...@ru...] > Sent: Tuesday, September 03, 2013 11:24 PM > To: psi...@li... > Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] New version 3.50.0 of > psi-ms.obo > > Hi Brian, > > yes we obsoletetd the retention time(s) term. > > Because we had two terms: retention time and retention time(s), we > decided to obsolete one and add a term named scan start time for the > SpectrumIdentificationResult annotation, see our discussion in Issue 74 > on google code: > > https://code.google.com/p/psi-pi/issues/detail?id=74&can=1 > > Best Regards, > Gerhard > > > Am 04.09.2013 00:38, schrieb Brian Pratt: > > I'm a little slow noticing this (just now updating ProteoWizard's > OBO), but > > I wonder about the now obsoleted > > id: MS:1001114 > > name: retention time(s) > > def: "Retention time of the spectrum from the source file." [PSI:PI] > > > > Surely chromatography and mass spec can happen in entirely different > time > > frames, as with MALDI - or am I misunderstanding something? > > > > And how is it different from > > id: MS:1000894 > > name: retention time > > def: "A measure of the interval relative to the beginning of a mass > > spectrometric run when a peptide will exit the chromatographic > column." > > [PSI:MS] > > > > And doesn't that definition have the same assumption about the column > being > > hooked up directly to the mass spec? > > > > Cheers, > > Brian Pratt > > > > > > On Fri, May 31, 2013 at 12:10 AM, Gerhard Mayer < > > Ger...@ru...> wrote: > > > >> Dear proteomics community, > >> > >> attached there's the new version 3.50.0 of the psi-ms.obo file. > >> > >> It contains the changes concerning the retention time terms (issue > 74), > >> changes for the waters instrument term definitions and 3 new terms > for the > >> Byonic search engine. > >> > >> > >> Changed CV terms in version 3.50.0 of psi-ms.obo: > >> ==============================**=================== > >> ************ added the two is_a relations 'is_a: MS:1001105 ! > peptide > >> result details' and > >> ************ 'is_a: MS:1001405 ! spectrum identification result > details' > >> [Term] > >> 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 > >> is_a: MS:1001105 ! peptide result details > >> is_a: MS:1001405 ! spectrum identification result details > >> relationship: has_units UO:0000010 ! second > >> relationship: has_units UO:0000031 ! minute > >> > >> ************ Made obsolete > >> [Term] > >> id: MS:1001114 > >> name: retention time(s) > >> def: "OBSOLETE Retention time of the spectrum from the source file." > >> [PSI:PI] > >> comment: This term was made obsolete because scan start time > (MS:1000016) > >> should be used instead. > >> xref: value-type:xsd\:double "The allowed value-type for this CV > term." > >> is_a: MS:1001105 ! peptide result details > >> is_a: MS:1001405 ! spectrum identification result details > >> relationship: has_units UO:0000010 ! second > >> relationship: has_units UO:0000031 ! minute > >> is_obsolete: true > >> > >> ************ Changed the definition (removed 'peptide ...'). > >> [Term] > >> id: MS:1000894 > >> name: retention time > >> def: "A measure of the interval relative to the beginning of a mass > >> spectrometric run." [PSI:MS] > >> is_a: MS:1000887 ! peptide attribute > >> > >> ************ Changed the is_a relationship from 'detector type' --> > 'array > >> detector' for the next two terms > >> [Term] > >> id: MS:1000114 > >> name: microchannel plate detector > >> def: "A thin plate that contains a closely spaced array of channels > that > >> each act as a continuous dynode particle multiplier. A charged > particle, > >> fast neutral particle, or photon striking the plate causes a cascade > of > >> secondary electrons that ultimately exits the opposite side of the > plate." > >> [PSI:MS] > >> synonym: "multichannel plate" EXACT [] > >> is_a: MS:1000345 ! array detector > >> > >> [Term] > >> id: MS:1000621 > >> name: photodiode array detector > >> def: "An array detector used to record spectra in the ultraviolet > and > >> visible region of light." [PSI:MS] > >> synonym: "PDA" EXACT [] > >> is_a: MS:1000345 ! array detector > >> > >> ************ Added the 'is_a: MS:1000621 ! photodiode array > detector' > >> relationship > >> [Term] > >> id: MS:1000818 > >> name: Acquity UPLC PDA > >> def: "Acquity UPLC Photodiode Array Detector." [PSI:MS] > >> is_a: MS:1000126 ! Waters instrument model > >> is_a: MS:1000621 ! photodiode array detector > >> > >> ************ Added the 'is_a: MS:1002308 ! fluorescence detector' > >> relationship > >> [Term] > >> id: MS:1000819 > >> name: Acquity UPLC FLR > >> def: "Acquity UPLC Fluorescence Detector." [PSI:MS] > >> is_a: MS:1000126 ! Waters instrument model > >> is_a: MS:1002308 ! fluorescence detector > >> > >> ************ Adapted the definitions for the following Waters > instruments > >> to be more specific and unambiguous: > >> MS:1000159 GCT > >> MS:1000170 M@LDI L > >> MS:1000171 M@LDI LR > >> MS:1000188 Q-Tof micro > >> MS:1000189 Q-Tof ultima > >> MS:1000191 quattro micro > >> MS:1000192 Quattro UItima > >> MS:1000632 Q-Tof Premier > >> MS:1001761 ACQUITY UPLC > >> MS:1001762 ACQUITY UPLC H-Class > >> MS:1001763 ACQUITY UPLC H-Class Bio > >> MS:1001764 ACQUITY UPLC I-Class > >> MS:1001765 ACQUITY UPLC Systems with 2D Technology > >> MS:1001766 nanoACQUITY UPLC > >> MS:1001767 nanoACQUITY UPLC System with Technology > >> MS:1001768 nanoACQUITY UPLC with HDX Technology > >> MS:1001769 TRIZAIC UPLC nanoTile > >> MS:1001770 GCT Premier > >> MS:1001771 MALDI Synapt G2 HDMS > >> MS:1001772 MALDI Synapt G2 MS > >> MS:1001773 MALDI Synapt G2-S HDMS > >> MS:1001774 MALDI Synapt G2-S MS > >> MS:1001775 MALDI Synapt HDMS > >> MS:1001776 MALDI Synapt MS > >> MS:1001777 Synapt G2 HDMS > >> MS:1001778 Synapt G2 MS > >> MS:1001779 Synapt G2-S HDMS > >> MS:1001780 Synapt G2-S MS > >> MS:1001781 Synapt HDMS > >> MS:1001782 Synapt MS > >> MS:1001783 Xevo G2 Q-Tof > >> MS:1001784 Xevo G2 Tof > >> MS:1001785 Xevo Q-Tof > >> MS:1001786 3100 > >> MS:1001787 Acquity SQD > >> MS:1001788 Acquity TQD > >> MS:1001789 Quattro micro GC > >> MS:1001790 Xevo TQ MS > >> MS:1001791 Xevo TQD > >> MS:1001792 Xevo TQ-S > >> MS:1001795 Empower > >> MS:1001796 Unify > >> > >> > >> New CV terms in version 3.50.0 of psi-ms.obo: > >> ==============================**=============== > >> [Term] > >> id: MS:1002308 > >> name: fluorescence detector > >> def: "A detector using a fluorescent signal after excitation with > light." > >> [PSI:MS] > >> is_a: MS:1000026 ! detector type > >> > >> [Term] > >> id: MS:1002309 > >> name: Byonic: Peptide AbsLogProb > >> def: "The absolute value of the log-base10 of the Byonic posterior > error > >> probability (PEP) of the PSM. " [PSI:PI] > >> xref: value-type:xsd\:double "The allowed value-type for this CV > term." > >> is_a: MS:1001143 ! search engine specific score for PSMs > >> is_a: MS:1001153 ! search engine specific score > >> has_order: MS:1002108 ! higher score better > >> > >> [Term] > >> id: MS:1002310 > >> name: Byonic: Protein AbsLogProb > >> def: "The absolute value of the log-base10 of the Byonic posterior > error > >> probability (PEP) of the protein. " [PSI:PI] > >> xref: value-type:xsd\:double "The allowed value-type for this CV > term." > >> is_a: MS:1001116 ! single protein result details > >> is_a: MS:1001153 ! search engine specific score > >> has_order: MS:1002108 ! higher score better > >> > >> [Term] > >> id: MS:1002311 > >> name: Byonic: Peptide AbsLogProb2D > >> def: "The absolute value of the log-base10 Byonic two-dimensional > >> posterior error probability (PEP) of the PSM. The two-dimensional > PEP takes > >> into account protein ranking information as well as PSM > information." > >> [PSI:PI] > >> xref: value-type:xsd\:double "The allowed value-type for this CV > term." > >> is_a: MS:1001143 ! search engine specific score for PSMs > >> is_a: MS:1001153 ! search engine specific score > >> has_order: MS:1002108 ! higher score better > >> > >> Best Regards, > >> Gerhard > >> > >> -- > >> --- > >> Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer > >> Bioinformatik / Biostatistik > >> Medizinisches-Proteom-Center (MPC) > >> Ruhr-Universität Bochum > >> Zentrum für klinische Forschung I (ZKF I) > >> E.049a > >> Universitätsstraße 150 > >> D-44801 Bochum > >> Phone: +49(0)234/32-21006 > >> Fax: +49(0)234/32-14554 > >> Email: Ger...@ru... > >> Web: http://www.medizinisches-**proteom- > center.de<http://www.medizinisches-proteom-center.de> > >> > >> > >> > >> -------------------------------------------------------------------- > ---------- > >> Get 100% visibility into Java/.NET code with AppDynamics Lite > >> It's a free troubleshooting tool designed for production > >> Get down to code-level detail for bottlenecks, with <2% overhead. > >> Download for free and get started troubleshooting in minutes. > >> http://p.sf.net/sfu/appdyn_d2d_ap2 > >> _______________________________________________ > >> Psidev-ms-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > >> > >> > > > > > > > > --------------------------------------------------------------------- > --------- > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, > more! > > Discover the easy way to master current and previous Microsoft > technologies > > and advance your career. Get an incredible 1,500+ hours of step-by- > step > > tutorial videos with LearnDevNow. Subscribe today and save! > > > http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.cl > ktrk > > > > > > > > _______________________________________________ > > Psidev-ms-vocab mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab > > > > > -- > --- > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer > Bioinformatik / Biostatistik > Medizinisches-Proteom-Center (MPC) > Ruhr-Universität Bochum > Zentrum für klinische Forschung I (ZKF I) > E.049a > Universitätsstraße 150 > D-44801 Bochum > > Phone: +49(0)234/32-21006 > Fax: +49(0)234/32-14554 > Email: Ger...@ru... > Web: http://www.medizinisches-proteom-center.de > > ----------------------------------------------------------------------- > ------- > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! > Discover the easy way to master current and previous Microsoft > technologies > and advance your career. Get an incredible 1,500+ hours of step-by-step > tutorial videos with LearnDevNow. 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