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Re: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans
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From: Eric D. <ede...@sy...> - 2016-10-05 21:33:33
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I’m a little confused, you say ‘instead of “is_a: MS:1000044 ! dissociation method”’ But as far as I see in the proposed entry that’s not the parent. But in any case, I’m fine with wherever Gerhard decides to parent it. Maybe he can weigh in on where he thinks it is best placed. Thanks! Eric *From:* Gibbons, Bryson C [mailto:bry...@pn...] *Sent:* Tuesday, October 04, 2016 9:46 PM *To:* Eric Deutsch; psi...@li... *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Yes, I agree that it would fix the situation. I don’t know that they have been used anywhere thus far (ProteoWizard doesn’t use them yet). The only other change might be to the “is_a” relationships, for consistency between the two supplemental activation types – like make the is_a relationship for MS:1002679 “is_a: MS:1000133 ! collision-induced dissociation” instead of “is_a: MS:1000044 ! dissociation method” Thank you. Bryson *From:* Eric Deutsch [mailto:ede...@sy... <ede...@sy...>] *Sent:* Tuesday, October 04, 2016 9:38 PM *To:* Gibbons, Bryson C <bry...@pn...>; psi...@li... *Cc:* Eric Deutsch <ede...@sy...> *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Okay, well maybe if we think the “higher energy” term has been misused in all instances thus far, maybe we should just keep the id and change the definition. What if we just changed the existing term to this: [Term] id: MS:1002678 name: supplemental beam-type collision-induced dissociation def: " A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation Would that fix the situation? Thanks, Eric *From:* Gibbons, Bryson C [mailto:bry...@pn...] *Sent:* Tuesday, October 04, 2016 3:30 PM *To:* Eric Deutsch; psi...@li... *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Okay, sorry for the lack of clarity… The HCD activation type in Thermo .raw files is translated into the CV term: [Term] id: MS:1000422 name: beam-type collision-induced dissociation def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS] synonym: "HCD" EXACT [] is_a: MS:1000133 ! collision-induced dissociation There is the separate term: [Term] id: MS:1002481 name: higher energy beam-type collision-induced dissociation def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation that was closely copied to create the term MS:1002678. Given the voltages used, I believe we actually need something close to the following: [Term] id: MS:100XXXX name: supplemental beam-type collision-induced dissociation def: "A supplemental collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS] is_a: MS:1000133 ! collision-induced dissociation -- and maybe this should be “is_a: MS:1002679 ! supplemental collision-induced dissociation”? Bryson *From:* Eric Deutsch [mailto:ede...@sy... <ede...@sy...>] *Sent:* Tuesday, October 04, 2016 3:16 PM *To:* Gibbons, Bryson C <bry...@pn...>; psi...@li... *Cc:* Eric Deutsch <ede...@sy...> *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Hi Bryson, I don’t quite understand what you mean here. Are you suggesting that we add a third term, or that our definition is poor? Here’s what we have: [Term] id: MS:1002678 name: supplemental higher energy beam-type collision-induced dissociation def: "A supplemental collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation [Term] id: MS:1002679 name: supplemental collision-induced dissociation def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS] is_a: MS:1000044 ! dissociation method Can you be more specific about what you’re proposing and why? Thanks, Eric *From:* Gibbons, Bryson C [mailto:bry...@pn...] *Sent:* Tuesday, October 04, 2016 2:28 PM *To:* Eric Deutsch; psi...@li... *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Looking at this now, I realized the one change I would have made is that we need “supplemental beam-type collision-induced dissociation”, which corresponds to the commonly used HCD; “supplemental higher energy beam-type collision-induced dissociation” (very high eV – 1000+, beyond the ~65eV that is actually used in the files I have looked at) was added instead. Bryson Gibbons *From:* Eric Deutsch [mailto:ede...@sy... <ede...@sy...>] *Sent:* Tuesday, June 07, 2016 1:58 PM *To:* psi...@li...; Gibbons, Bryson C < bry...@pn...> *Cc:* Eric Deutsch <ede...@sy...> *Subject:* RE: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans So the proposal is this? <activation> <cvParam cvRef="MS" accession="MS:1000598" name="electron transfer dissociation"/> <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="53.58" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/> <cvParam cvRef="MS" accession="MS:100????" name="supplemental higher energy beam-type collision-induced dissociation"/> <cvParam cvRef="MS" accession="MS:100????" name="supplemental collision energy" value="20" unitCvRef="UO" unitAccession="UO:0000266" unitName="electronvolt"/> </activation> Thanks, Eric *From:* Chambers, Matthew [mailto:mat...@gm...] *Sent:* Tuesday, June 07, 2016 1:40 PM *To:* Gibbons, Bryson C; psi...@li... *Subject:* Re: [Psidev-ms-vocab] [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Moving this discussion about having separate activation energies for primary and supplemental activations to psidev-ms-vocab. Most of the rules about what you can do in mzML are encoded in the CV mapping file, not the schema. A supplemental activation energy cvParam could indeed be useful, but by itself it would assume the reader knows which activation method is the primary and which is supplemental. :) But since there are a small number of supplemental activation types (e.g. CID and HCD, and what else?), we could create derived terms from the main CID and HCD terms and prefix them with "supplemental". To get any cleaner it may need to be a schema change, and that's a big hurdle. -Matt On 6/7/2016 3:31 PM, Gibbons, Bryson C wrote: According to what I can see at http://www.peptideatlas.org/tmp/mzML1.1.0.html#activation, you could possibly list 2 cvParams for activation energy and be schema-compliant, but that’s almost worse because you wouldn’t have a clear image of what activation energy corresponds to which activation type. It would be useful if there was a “supplemental activation energy” cvParam. Bryson *From:* Chambers, Matthew [mailto:mat...@gm... <mat...@gm...>] *Sent:* Tuesday, June 07, 2016 1:18 PM *To:* Gibbons, Bryson C <bry...@pn...> <bry...@pn...>; pro...@li... *Subject:* Re: [proteowizard-support] msconvert/pwiz_bindings_cli - Activation energy missing on Thermo ETD scans Another problem is that I'm not aware of any CV-conformant way to have multiple precursor activation energies in mzML for combined activation modes. We could put the ETD energy in as a userParam, but just putting another collision energy CV param in there is not correct. On 6/7/2016 2:01 PM, Gibbons, Bryson C wrote: ITMS + c NSI r d sa Full ms2 407.5405@etd53.58@hcd20.00 [120.0000-1233.0000] |