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From: Alexander L. <le...@im...> - 2017-01-16 15:34:30
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Hi Andy, I looked through the response letter and am fine with the text and all changes made to the manuscript. Regarding the implementation of an mzIdentML export feature for xQuest, we are working with the OpenMS team (especially Eugen), and hopefully there will be some way to convert the current XML output of xQuest into mzIdentML 1.2. In short, I would consider it "in progress". Best regards, Alexander Jones, Andy schrieb: > > Hi all, > > (Sent to PSI-PI mailing list plus authors of the mzid paper, in case > any of you are not on the mailing list). > > We have received 5 reviews of the mzid 1.2 specifications via the PSI > process, as well as the 2 reviews received on the manuscript from MCP, > for which it makes sense to consider together. I think most of these > can be addressed fairly simply. I have already fixed a few typos in > the specification document that were identified, and made one or two > other sensible clarifications to wording. These changes have been > checked into GitHub. I have started response documents to both > processes in the relevant zip files. > > *If you would like to contribute, please could you send me any > feedback within one week (by 19^th Jan) if possible. *After that > point, I will submit the mzid 1.2 specs back to the PSI process (for > which Sylvie the editor recommended minor corrections), unless > anything comes up that needs extensive further discussion. Once they > are accepted, I will resubmit the paper to MCP, as reporting the mzid > 1.2 final specifications. > > Just flagging a few points for specific people to address: > > -Robert and Alexander: one of the reviewer asks whether your > cross-linking software will export mzid 1.2, anything you can say here? > > -Fawaz – one of the reviewers seemed to find some validation errors > with some of our mzid 1.2 files, please could you take a look > > -Juan – one of the MCP reviewers suggests we change the figures. Can > you give me a view on whether you think we need to do this? I’m of the > view to make minor improvements, but not radically change them. > > -Gerhard – see response to MCP reviews. One of the reviewers would > like to know how spectral counts can be added at the peptide-level. I > think this may need a new parent term for one given CV term (see my > notes in the response to reviews doc), could you take a look? > > Best wishes > > Andy > |
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From: mayerg97 <ger...@ru...> - 2017-01-17 12:54:52
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Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: > > Hi all, > > (Sent to PSI-PI mailing list plus authors of the mzid paper, in case > any of you are not on the mailing list). > > We have received 5 reviews of the mzid 1.2 specifications via the PSI > process, as well as the 2 reviews received on the manuscript from MCP, > for which it makes sense to consider together. I think most of these > can be addressed fairly simply. I have already fixed a few typos in > the specification document that were identified, and made one or two > other sensible clarifications to wording. These changes have been > checked into GitHub. I have started response documents to both > processes in the relevant zip files. > > *If you would like to contribute, please could you send me any > feedback within one week (by 19^th Jan) if possible. *After that > point, I will submit the mzid 1.2 specs back to the PSI process (for > which Sylvie the editor recommended minor corrections), unless > anything comes up that needs extensive further discussion. Once they > are accepted, I will resubmit the paper to MCP, as reporting the mzid > 1.2 final specifications. > > Just flagging a few points for specific people to address: > > -Robert and Alexander: one of the reviewer asks whether your > cross-linking software will export mzid 1.2, anything you can say here? > > -Fawaz – one of the reviewers seemed to find some validation errors > with some of our mzid 1.2 files, please could you take a look > > -Juan – one of the MCP reviewers suggests we change the figures. Can > you give me a view on whether you think we need to do this? I’m of the > view to make minor improvements, but not radically change them. > > -Gerhard – see response to MCP reviews. One of the reviewers would > like to know how spectral counts can be added at the peptide-level. I > think this may need a new parent term for one given CV term (see my > notes in the response to reviews doc), could you take a look? > > Best wishes > > Andy > -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Eric D. <ede...@sy...> - 2017-01-17 15:32:11
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This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, January 17, 2017 4:39 AM *To:* Jones, Andy; psi...@li... *Cc:* Juan Antonio Vizcaino (ju...@eb...); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...; jul...@ru...; mar...@ru...; lfi...@st...; ju...@ed...; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...; 'Eric Deutsch; psi...@li... *Subject:* Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. *If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. *After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de |
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From: Juan A. V. <ju...@eb...> - 2017-01-18 09:42:30
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Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan > On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...> wrote: > > This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. > > Thanks, > Eric > > > From: mayerg97 [mailto:ger...@ru... <mailto:ger...@ru...>] > Sent: Tuesday, January 17, 2017 4:39 AM > To: Jones, Andy; psi...@li... <mailto:psi...@li...> > Cc: Juan Antonio Vizcaino (ju...@eb... <mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb... <mailto:to...@eb...>; jul...@ru... <mailto:jul...@ru...>; mar...@ru... <mailto:mar...@ru...>; lfi...@st... <mailto:lfi...@st...>; ju...@ed... <mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im... <mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr... <mailto:sma...@pr...>; 'Eric Deutsch; psi...@li... <mailto:psi...@li...> > Subject: Re: mzid 1.2 reviews > > Hi Andy, > > yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25 <https://github.com/HUPO-PSI/mzIdentML/issues/25>, > but I think this problem is not related to the restructuring. > > What about > > [Term] > id: MS:1001842 > name: peptide PSM count > def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > Best regards, > Gerhard > > > > Am 11.01.2017 um 16:56 schrieb Jones, Andy: >> Hi all, >> >> (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). >> >> We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. >> >> If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. >> >> Just flagging a few points for specific people to address: >> >> - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? >> - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look >> - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. >> - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? >> >> Best wishes >> Andy >> >> >> >> > > -- > -------------------------------------------------------------------- > > Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER > > PhD student > > Medizinisches Proteom-Center > > DEPARTMENT Medical Bioinformatics > > Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 > > E-mail ger...@ru... <mailto:ger...@ru...> > www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Eric D. <ede...@sy...> - 2017-01-18 17:18:18
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Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: name: distinct peptide sequence-level spectral count name: modified peptide sequence-level spectral count name: peptide ion-level spectral count What do you think? Does this capture the desired concepts clearly? Regards, Eric *From:* Juan Antonio Vizcaino [mailto:ju...@eb...] *Sent:* Wednesday, January 18, 2017 1:42 AM *To:* Eric Deutsch <ede...@sy...> *Cc:* mayerg97 <ger...@ru...>; Andy Jones < And...@li...>; psi...@li...; Perkins, Simon <Sim...@li...>; Harald Barsnes < Har...@ui...>; Yasset Perez-Riverol <yp...@eb...>; Tobias Ternent <to...@eb...>; jul...@ru...; mar...@ru...; lfi...@st...; ju...@ed...; Eugen Netz <eug...@tu...>; Mathias Walzer < wa...@in...>; Oliver Kohlbacher < oli...@un...>; le...@im...; Robert Chalkley <cha...@cg...>; Ghali, Fawaz <F....@li...>; Salvador Martínez de Bartolomé <sma...@pr...>; psi...@li... *Subject:* Re: mzid 1.2 reviews Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...> wrote: This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, January 17, 2017 4:39 AM *To:* Jones, Andy; psi...@li... *Cc:* Juan Antonio Vizcaino (ju...@eb...); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...; jul...@ru...; mar...@ru...; lfi...@st...; ju...@ed...; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...; 'Eric Deutsch; psi...@li... *Subject:* Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. *If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. *After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de |
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From: Juan A. V. <ju...@eb...> - 2017-01-18 17:23:08
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Fine for me. Sorry, I did not realise about what Eric mentioned. He is completely right. Cheers, Juan > On 18 Jan 2017, at 17:18, Eric Deutsch <ede...@sy...> wrote: > > Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. > > May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: > > name: distinct peptide sequence-level spectral count > name: modified peptide sequence-level spectral count > name: peptide ion-level spectral count > > What do you think? Does this capture the desired concepts clearly? > > Regards, > Eric > > > > From: Juan Antonio Vizcaino [mailto:ju...@eb... <mailto:ju...@eb...>] > Sent: Wednesday, January 18, 2017 1:42 AM > To: Eric Deutsch <ede...@sy... <mailto:ede...@sy...>> > Cc: mayerg97 <ger...@ru... <mailto:ger...@ru...>>; Andy Jones <And...@li... <mailto:And...@li...>>; psi...@li... <mailto:psi...@li...>; Perkins, Simon <Sim...@li... <mailto:Sim...@li...>>; Harald Barsnes <Har...@ui... <mailto:Har...@ui...>>; Yasset Perez-Riverol <yp...@eb... <mailto:yp...@eb...>>; Tobias Ternent <to...@eb... <mailto:to...@eb...>>; jul...@ru... <mailto:jul...@ru...>; mar...@ru... <mailto:mar...@ru...>; lfi...@st... <mailto:lfi...@st...>; ju...@ed... <mailto:ju...@ed...>; Eugen Netz <eug...@tu... <mailto:eug...@tu...>>; Mathias Walzer <wa...@in... <mailto:wa...@in...>>; Oliver Kohlbacher <oli...@un... <mailto:oli...@un...>>; le...@im... <mailto:le...@im...>; Robert Chalkley <cha...@cg... <mailto:cha...@cg...>>; Ghali, Fawaz <F....@li... <mailto:F....@li...>>; Salvador Martínez de Bartolomé <sma...@pr... <mailto:sma...@pr...>>; psi...@li... <mailto:psi...@li...> > Subject: Re: mzid 1.2 reviews > > Hi all, > > I agree with Eric on this. The more clarity the better. What about? > > [Term] > id: MS:1001842 > name: peptide PSM count (peptide as the raw peptide sequence) > def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination between peptide sequence and modifications) > def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) > def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. > > What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. > > Cheers, > > Juan > > > >> On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy... <mailto:ede...@sy...>> wrote: >> >> This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. >> >> Thanks, >> Eric >> >> >> From: mayerg97 [mailto:ger...@ru... <mailto:ger...@ru...>] >> Sent: Tuesday, January 17, 2017 4:39 AM >> To: Jones, Andy; psi...@li... <mailto:psi...@li...> >> Cc: Juan Antonio Vizcaino (ju...@eb... <mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb... <mailto:to...@eb...>; jul...@ru... <mailto:jul...@ru...>; mar...@ru... <mailto:mar...@ru...>; lfi...@st... <mailto:lfi...@st...>; ju...@ed... <mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im... <mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr... <mailto:sma...@pr...>; 'Eric Deutsch; psi...@li... <mailto:psi...@li...> >> Subject: Re: mzid 1.2 reviews >> >> Hi Andy, >> >> yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25 <https://github.com/HUPO-PSI/mzIdentML/issues/25>, >> but I think this problem is not related to the restructuring. >> >> What about >> >> [Term] >> id: MS:1001842 >> name: peptide PSM count >> def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] >> xref: value-type:xsd\:int "The allowed value-type for this CV term." >> is_a: MS:1001805 ! quantification datatype >> is_a: MS:1002015 ! spectral count peptide level quantitation >> >> Best regards, >> Gerhard >> >> >> Am 11.01.2017 um 16:56 schrieb Jones, Andy: >>> Hi all, >>> >>> (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). >>> >>> We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. >>> >>> If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. >>> >>> Just flagging a few points for specific people to address: >>> >>> - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? >>> - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look >>> - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. >>> - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? >>> >>> Best wishes >>> Andy >>> >>> >>> >>> >> >> -- >> -------------------------------------------------------------------- >> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER >> PhD student >> Medizinisches Proteom-Center >> DEPARTMENT Medical Bioinformatics >> Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum >> Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 >> E-mail ger...@ru... <mailto:ger...@ru...> >> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Binz Pierre-A. <Pie...@ch...> - 2017-01-19 08:51:37
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Hi all, Yep, we are redundantly coming to thosse definitions and interpretations of what those peptidic things are... A peptide is, according to IUPAC gold book https://goldbook.iupac.org/P04479.html: Peptides : Amides<https://goldbook.iupac.org/A00266.html> derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond<https://goldbook.iupac.org/C01384.html> from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. Therefore it includes a combination of all 20 amino acids + all kinds of modifications A peptide is not a peptide ion in the sense of a MS ion as it is usually the charge neutral representation of a combination of a-aminoacids in the case of protein peptides What we represent here are either the molecular ion (peptide sequence represented by one-letter codes + optional PTMs + charged aduct (H+) + charge state) which we can call peptide ion : [ANSpK +2H] 2+ (where Sp is a phosphoserine) which we can interpret with only the sequence with PTMs ANSpK or only with the primary sequence with no PTM ANSK My suggestion then is to keep the term peptide as the most generic and does not need to specify whether it carries PTMs or not: name: peptide-level spectral count # of ANSpK name: sequence-level spectral count # of ANSK name: peptide ion-level spectral count # of [ANSpK+2H]2+ Now if you feel that the term “peptide-level” will be ambiguous (people will not know that peptide sequence and peptide (with or without mods) are different, we can give a clear definition with example or I could recommend using “peptide form level” or “peptide species level” as analogy to protein form or protein species vs protein (top-down inspired definition), but this adds a new definition and make our filkes larger for no good reasons. Pierre-Alain De : Juan Antonio Vizcaino [mailto:ju...@eb...] Envoyé : mercredi 18 janvier 2017 18:23 À : Eric Deutsch Cc : Tobias Ternent; psi...@li...; Robert Chalkley; le...@im...; jul...@ru...; Ghali, Fawaz; mar...@ru...; mayerg97; Andy Jones; Perkins, Simon; psi...@li...; ju...@ed...; Eugen Netz; Harald Barsnes Objet : Re: [Psidev-pi-dev] mzid 1.2 reviews Fine for me. Sorry, I did not realise about what Eric mentioned. He is completely right. Cheers, Juan On 18 Jan 2017, at 17:18, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: name: distinct peptide sequence-level spectral count name: modified peptide sequence-level spectral count name: peptide ion-level spectral count What do you think? Does this capture the desired concepts clearly? Regards, Eric From: Juan Antonio Vizcaino [mailto:ju...@eb...<mailto:ju...@eb...>] Sent: Wednesday, January 18, 2017 1:42 AM To: Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> Cc: mayerg97 <ger...@ru...<mailto:ger...@ru...>>; Andy Jones <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...>; Perkins, Simon <Sim...@li...<mailto:Sim...@li...>>; Harald Barsnes <Har...@ui...<mailto:Har...@ui...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; Tobias Ternent <to...@eb...<mailto:to...@eb...>>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz <eug...@tu...<mailto:eug...@tu...>>; Mathias Walzer <wa...@in...<mailto:wa...@in...>>; Oliver Kohlbacher <oli...@un...<mailto:oli...@un...>>; le...@im...<mailto:le...@im...>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Ghali, Fawaz <F....@li...<mailto:F....@li...>>; Salvador Martínez de Bartolomé <sma...@pr...<mailto:sma...@pr...>>; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric From: mayerg97 [mailto:ger...@ru...<mailto:ger...@ru...>] Sent: Tuesday, January 17, 2017 4:39 AM To: Jones, Andy; psi...@li...<mailto:psi...@li...> Cc: Juan Antonio Vizcaino (ju...@eb...<mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...<mailto:to...@eb...>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...<mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...<mailto:sma...@pr...>; 'Eric Deutsch; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2017-01-20 09:59:52
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Hello all, so according Pierre-Alains proposal we would have [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation any futher comments? Best regards, Gerhard Am 19.01.2017 um 09:16 schrieb Binz Pierre-Alain: > > Hi all, > > Yep, we are redundantly coming to thosse definitions and > interpretations of what those peptidic things are... > > > A peptide is, according to IUPAC gold book > https://goldbook.iupac.org/P04479.html: > > > Peptides : Amides <https://goldbook.iupac.org/A00266.html> derived > from two or more amino carboxylic acid molecules (the same or > different) by formation of a covalent bond > <https://goldbook.iupac.org/C01384.html> from the carbonyl carbon of > one to the nitrogen atom of another with formal loss of water. The > term is usually applied to structures formed from α-amino acids, but > it includes those derived from any amino carboxylic acid. > > Therefore it includes a combination of all 20 amino acids + all kinds > of modifications > > A peptide is not a peptide ion in the sense of a MS ion as it is > usually the charge neutral representation of a combination of > a-aminoacids in the case of protein peptides > > What we represent here are either the molecular ion (peptide sequence > represented by one-letter codes + optional PTMs + charged aduct (H+) + > charge state) which we can call peptide ion : [ANSpK +2H] 2+ (where > Sp is a phosphoserine) which we can interpret with only the sequence > with PTMs ANSpK or only with the primary sequence with no PTM ANSK > > My suggestion then is to keep the term peptide as the most generic and > does not need to specify whether it carries PTMs or not: > > name: peptide-level spectral > count # of ANSpK > > name: sequence-level spectral count > # of ANSK > > name: peptide ion-level spectral > count # of [ANSpK+2H]2+ > > Now if you feel that the term “peptide-level” will be ambiguous > (people will not know that peptide sequence and peptide (with or > without mods) are different, we can give a clear definition with > example or I could recommend using “peptide form level” or “peptide > species level” as analogy to protein form or protein species vs > protein (top-down inspired definition), but this adds a new > definition and make our filkes larger for no good reasons. > > Pierre-Alain > > *De :*Juan Antonio Vizcaino [mailto:ju...@eb...] > *Envoyé :* mercredi 18 janvier 2017 18:23 > *À :* Eric Deutsch > *Cc :* Tobias Ternent; psi...@li...; Robert > Chalkley; le...@im...; > jul...@ru...; Ghali, Fawaz; > mar...@ru...; mayerg97; Andy Jones; Perkins, Simon; > psi...@li...; ju...@ed...; Eugen Netz; Harald > Barsnes > *Objet :* Re: [Psidev-pi-dev] mzid 1.2 reviews > > Fine for me. Sorry, I did not realise about what Eric mentioned. He is > completely right. > > Cheers, > > Juan > > On 18 Jan 2017, at 17:18, Eric Deutsch > <ede...@sy... <mailto:ede...@sy...>> > wrote: > > Hi everyone, I agree that splitting this into 3 terms is good. I > disagree that we should misuse the term “peptide” and then try to > clarify it with a parenthetical expression. I don’t think this is > good controlled vocabulary practice. I suspect the true ontology > devotees would be horrified by this practice. > > May I suggest that we use the style that I adopted for the > mzIdentML CV reorg? This keeps the term name concise, and we > should rely on the definition to remove any ambiguity. I suggest > these names instead: > > name: distinct peptide sequence-level spectral count > > name: modified peptide sequence-level spectral count > name: peptide ion-level spectral count > > What do you think? Does this capture the desired concepts clearly? > > Regards, > > Eric > > *From:*Juan Antonio Vizcaino [mailto:ju...@eb... > <mailto:ju...@eb...>] > *Sent:*Wednesday, January 18, 2017 1:42 AM > *To:*Eric Deutsch <ede...@sy... > <mailto:ede...@sy...>> > *Cc:*mayerg97 <ger...@ru... > <mailto:ger...@ru...>>; Andy Jones > <And...@li... > <mailto:And...@li...>>;psi...@li... > <mailto:psi...@li...>; Perkins, Simon > <Sim...@li... > <mailto:Sim...@li...>>; Harald Barsnes > <Har...@ui... <mailto:Har...@ui...>>; Yasset > Perez-Riverol <yp...@eb... <mailto:yp...@eb...>>; Tobias > Ternent <to...@eb... > <mailto:to...@eb...>>;jul...@ru... > <mailto:jul...@ru...>;mar...@ru... > <mailto:mar...@ru...>;lfi...@st... > <mailto:lfi...@st...>;ju...@ed... > <mailto:ju...@ed...>; Eugen Netz <eug...@tu... > <mailto:eug...@tu...>>; Mathias Walzer > <wa...@in... > <mailto:wa...@in...>>; Oliver Kohlbacher > <oli...@un... > <mailto:oli...@un...>>;le...@im... > <mailto:le...@im...>; Robert Chalkley > <cha...@cg... <mailto:cha...@cg...>>; Ghali, > Fawaz <F....@li... <mailto:F....@li...>>; > Salvador Martínez de Bartolomé <sma...@pr... > <mailto:sma...@pr...>>;psi...@li... > <mailto:psi...@li...> > *Subject:*Re: mzid 1.2 reviews > > Hi all, > > I agree with Eric on this. The more clarity the better. What about? > > [Term] > id: MS:1001842 > name: peptide PSM count (peptide as the raw peptide sequence) > > def: "The number of MS2 spectra identified for a given peptide > (considering the raw peptide sequence, and merging all charge > states, modifications in the same peptide sequence are not > considered separately) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination between > peptide sequence and modifications) > def: "The number of MS2 spectra identified for a given peptide > (considering the peptide sequence plus modifications, and merging > all charge states) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination > between peptide sequence, modifications and charge state) > > def: "The number of MS2 spectra identified for a given peptide > (considering the peptide sequence and modifications, and one > single charge state) in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > Of course more variants would need to be created if we would want > to mix the definitions above with different charge states, but I > think these three definitions would be ok. > > What happens also in the case of ambiguity in the modification > position? So, it could be even more complex. But I think this > level is probably ok for the current state of things. > > Cheers, > > Juan > > On 17 Jan 2017, at 15:08, Eric Deutsch > <ede...@sy... > <mailto:ede...@sy...>> wrote: > > This is pretty good, but I think we should make it completely > clear whether it is the number of PSMs per peptide sequence, > per peptide with modifications, or per peptide ion (including > separate charge states). The plain word peptide is often used > as a standin for any of these 3 concepts.. > > Thanks, > > Eric > > *From:*mayerg97 [mailto:ger...@ru... > <mailto:ger...@ru...>] > *Sent:*Tuesday, January 17, 2017 4:39 AM > *To:*Jones, Andy;psi...@li... > <mailto:psi...@li...> > *Cc:*Juan Antonio Vizcaino (ju...@eb... > <mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; > 'Yasset Perez-Riverol';to...@eb... > <mailto:to...@eb...>;jul...@ru... > <mailto:jul...@ru...>;mar...@ru... > <mailto:mar...@ru...>;lfi...@st... > <mailto:lfi...@st...>;ju...@ed... > <mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver > Kohlbacher;le...@im... > <mailto:le...@im...>; 'Robert Chalkley'; Ghali, > Fawaz;sma...@pr... > <mailto:sma...@pr...>; 'Eric > Deutsch;psi...@li... > <mailto:psi...@li...> > *Subject:*Re: mzid 1.2 reviews > > Hi Andy, > > yes we did a CV restructuring, > seehttps://github.com/HUPO-PSI/mzIdentML/issues/25, > but I think this problem is not related to the restructuring. > > What about > > [Term] > id: MS:1001842 > name: peptide PSM count > def: "The number of MS2 spectra identified for this peptide in > spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV > term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > Best regards, > Gerhard > > Am 11.01.2017 um 16:56 schrieb Jones, Andy: > > Hi all, > > (Sent to PSI-PI mailing list plus authors of the mzid > paper, in case any of you are not on the mailing list). > > We have received 5 reviews of the mzid 1.2 specifications > via the PSI process, as well as the 2 reviews received on > the manuscript from MCP, for which it makes sense to > consider together. I think most of these can be addressed > fairly simply. I have already fixed a few typos in the > specification document that were identified, and made one > or two other sensible clarifications to wording. These > changes have been checked into GitHub. I have started > response documents to both processes in the relevant zip > files. > > *If you would like to contribute, please could you send me > any feedback within one week (by 19^th Jan) if > possible.*After that point, I will submit the mzid 1.2 > specs back to the PSI process (for which Sylvie the editor > recommended minor corrections), unless anything comes up > that needs extensive further discussion. Once they are > accepted, I will resubmit the paper to MCP, as reporting > the mzid 1.2 final specifications. > > Just flagging a few points for specific people to address: > > -Robert and Alexander: one of the reviewer asks whether > your cross-linking software will export mzid 1.2, anything > you can say here? > > -Fawaz – one of the reviewers seemed to find some > validation errors with some of our mzid 1.2 files, please > could you take a look > > -Juan – one of the MCP reviewers suggests we change the > figures. Can you give me a view on whether you think we > need to do this? I’m of the view to make minor > improvements, but not radically change them. > > -Gerhard – see response to MCP reviews. One of the > reviewers would like to know how spectral counts can be > added at the peptide-level. I think this may need a new > parent term for one given CV term (see my notes in the > response to reviews doc), could you take a look? > > Best wishes > > Andy > > -- > > *--------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building*ZKF E.049a|Universitätsstraße 150 | D-44801 Bochum > > *Fon*+49 (0)234 32-21006|*Fax*+49 (0)234 32-14554 > > *E-mail*ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de/> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-ms-vocab mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Jones, A. <And...@li...> - 2017-01-20 11:24:33
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Hi Gerhard, Thanks for this. Can I check – we want to have these as peptide-level data types. Can you recall the mapping mechanism that would tell reading software that these are for peptides rather than PSMs i.e. they would be repeated for all the PSMs grouped as the same peptide? The parent terms are not completely clear to me. Best wishes Andy From: mayerg97 [mailto:ger...@ru...] Sent: 20 January 2017 09:41 To: psi...@li...; psi...@li...; psi...@li... Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews Hello all, so according Pierre-Alains proposal we would have [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation any futher comments? Best regards, Gerhard Am 19.01.2017 um 09:16 schrieb Binz Pierre-Alain: Hi all, Yep, we are redundantly coming to thosse definitions and interpretations of what those peptidic things are... A peptide is, according to IUPAC gold book https://goldbook.iupac.org/P04479.html: Peptides : Amides<https://goldbook.iupac.org/A00266.html> derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond<https://goldbook.iupac.org/C01384.html> from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. Therefore it includes a combination of all 20 amino acids + all kinds of modifications A peptide is not a peptide ion in the sense of a MS ion as it is usually the charge neutral representation of a combination of a-aminoacids in the case of protein peptides What we represent here are either the molecular ion (peptide sequence represented by one-letter codes + optional PTMs + charged aduct (H+) + charge state) which we can call peptide ion : [ANSpK +2H] 2+ (where Sp is a phosphoserine) which we can interpret with only the sequence with PTMs ANSpK or only with the primary sequence with no PTM ANSK My suggestion then is to keep the term peptide as the most generic and does not need to specify whether it carries PTMs or not: name: peptide-level spectral count # of ANSpK name: sequence-level spectral count # of ANSK name: peptide ion-level spectral count # of [ANSpK+2H]2+ Now if you feel that the term “peptide-level” will be ambiguous (people will not know that peptide sequence and peptide (with or without mods) are different, we can give a clear definition with example or I could recommend using “peptide form level” or “peptide species level” as analogy to protein form or protein species vs protein (top-down inspired definition), but this adds a new definition and make our filkes larger for no good reasons. Pierre-Alain De : Juan Antonio Vizcaino [mailto:ju...@eb...] Envoyé : mercredi 18 janvier 2017 18:23 À : Eric Deutsch Cc : Tobias Ternent; psi...@li...<mailto:psi...@li...>; Robert Chalkley; le...@im...<mailto:le...@im...>; jul...@ru...<mailto:jul...@ru...>; Ghali, Fawaz; mar...@ru...<mailto:mar...@ru...>; mayerg97; Andy Jones; Perkins, Simon; psi...@li...<mailto:psi...@li...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz; Harald Barsnes Objet : Re: [Psidev-pi-dev] mzid 1.2 reviews Fine for me. Sorry, I did not realise about what Eric mentioned. He is completely right. Cheers, Juan On 18 Jan 2017, at 17:18, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: name: distinct peptide sequence-level spectral count name: modified peptide sequence-level spectral count name: peptide ion-level spectral count What do you think? Does this capture the desired concepts clearly? Regards, Eric From: Juan Antonio Vizcaino [mailto:ju...@eb...<mailto:ju...@eb...>] Sent: Wednesday, January 18, 2017 1:42 AM To: Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> Cc: mayerg97 <ger...@ru...<mailto:ger...@ru...>>; Andy Jones <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...>; Perkins, Simon <Sim...@li...<mailto:Sim...@li...>>; Harald Barsnes <Har...@ui...<mailto:Har...@ui...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; Tobias Ternent <to...@eb...<mailto:to...@eb...>>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz <eug...@tu...<mailto:eug...@tu...>>; Mathias Walzer <wa...@in...<mailto:wa...@in...>>; Oliver Kohlbacher <oli...@un...<mailto:oli...@un...>>; le...@im...<mailto:le...@im...>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Ghali, Fawaz <F....@li...<mailto:F....@li...>>; Salvador Martínez de Bartolomé <sma...@pr...<mailto:sma...@pr...>>; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric From: mayerg97 [mailto:ger...@ru...<mailto:ger...@ru...>] Sent: Tuesday, January 17, 2017 4:39 AM To: Jones, Andy; psi...@li...<mailto:psi...@li...> Cc: Juan Antonio Vizcaino (ju...@eb...<mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...<mailto:to...@eb...>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...<mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...<mailto:sma...@pr...>; 'Eric Deutsch; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-vocab mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> |
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From: Eric D. <ede...@sy...> - 2017-01-20 18:12:57
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I think I would prefer the longer, somewhat more pedantic and explicit names, but I am content enough with these if these have broader support. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Friday, January 20, 2017 1:41 AM *To:* psi...@li...; psi...@li...; psi...@li... *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews Hello all, so according Pierre-Alains proposal we would have [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation any futher comments? Best regards, Gerhard Am 19.01.2017 um 09:16 schrieb Binz Pierre-Alain: Hi all, Yep, we are redundantly coming to thosse definitions and interpretations of what those peptidic things are... A peptide is, according to IUPAC gold book https://goldbook.iupac.org/P04479.html:Peptides : Amides <https://goldbook.iupac.org/A00266.html> derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond <https://goldbook.iupac.org/C01384.html> from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. Therefore it includes a combination of all 20 amino acids + all kinds of modifications A peptide is not a peptide ion in the sense of a MS ion as it is usually the charge neutral representation of a combination of a-aminoacids in the case of protein peptides What we represent here are either the molecular ion (peptide sequence represented by one-letter codes + optional PTMs + charged aduct (H+) + charge state) which we can call peptide ion : [ANSpK +2H] 2+ (where Sp is a phosphoserine) which we can interpret with only the sequence with PTMs ANSpK or only with the primary sequence with no PTM ANSK My suggestion then is to keep the term peptide as the most generic and does not need to specify whether it carries PTMs or not: name: peptide-level spectral count # of ANSpK name: sequence-level spectral count # of ANSK name: peptide ion-level spectral count # of [ANSpK+2H]2+ Now if you feel that the term “peptide-level” will be ambiguous (people will not know that peptide sequence and peptide (with or without mods) are different, we can give a clear definition with example or I could recommend using “peptide form level” or “peptide species level” as analogy to protein form or protein species vs protein (top-down inspired definition), but this adds a new definition and make our filkes larger for no good reasons. Pierre-Alain *De :* Juan Antonio Vizcaino [mailto:ju...@eb... <ju...@eb...>] *Envoyé :* mercredi 18 janvier 2017 18:23 *À :* Eric Deutsch *Cc :* Tobias Ternent; psi...@li...; Robert Chalkley; le...@im...; jul...@ru...; Ghali, Fawaz; mar...@ru...; mayerg97; Andy Jones; Perkins, Simon; psi...@li...; ju...@ed...; Eugen Netz; Harald Barsnes *Objet :* Re: [Psidev-pi-dev] mzid 1.2 reviews Fine for me. Sorry, I did not realise about what Eric mentioned. He is completely right. Cheers, Juan On 18 Jan 2017, at 17:18, Eric Deutsch <ede...@sy...> wrote: Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: name: distinct peptide sequence-level spectral count name: modified peptide sequence-level spectral count name: peptide ion-level spectral count What do you think? Does this capture the desired concepts clearly? Regards, Eric *From:* Juan Antonio Vizcaino [mailto:ju...@eb...] *Sent:* Wednesday, January 18, 2017 1:42 AM *To:* Eric Deutsch <ede...@sy...> *Cc:* mayerg97 <ger...@ru...>; Andy Jones < And...@li...>; psi...@li...; Perkins, Simon <Sim...@li...>; Harald Barsnes < Har...@ui...>; Yasset Perez-Riverol <yp...@eb...>; Tobias Ternent <to...@eb...>; jul...@ru...; mar...@ru...; lfi...@st...; ju...@ed...; Eugen Netz <eug...@tu...>; Mathias Walzer < wa...@in...>; Oliver Kohlbacher < oli...@un...>; le...@im...; Robert Chalkley <cha...@cg...>; Ghali, Fawaz <F....@li...>; Salvador Martínez de Bartolomé <sma...@pr...>; psi...@li... *Subject:* Re: mzid 1.2 reviews Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...> wrote: This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, January 17, 2017 4:39 AM *To:* Jones, Andy; psi...@li... *Cc:* Juan Antonio Vizcaino (ju...@eb...); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...; jul...@ru...; mar...@ru...; lfi...@st...; ju...@ed...; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...; 'Eric Deutsch; psi...@li... *Subject:* Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. *If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. *After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-vocab mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de |
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From: Jones, A. <And...@li...> - 2017-01-23 13:43:36
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These seem okay to me. Best wishes Andy From: Eric Deutsch [mailto:ede...@sy...] Sent: 20 January 2017 17:42 To: psi...@li...; psi...@li...; psi...@li... Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews I think I would prefer the longer, somewhat more pedantic and explicit names, but I am content enough with these if these have broader support. Thanks, Eric From: mayerg97 [mailto:ger...@ru...<mailto:ger...@ru...>] Sent: Friday, January 20, 2017 1:41 AM To: psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews Hello all, so according Pierre-Alains proposal we would have [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation any futher comments? Best regards, Gerhard Am 19.01.2017 um 09:16 schrieb Binz Pierre-Alain: Hi all, Yep, we are redundantly coming to thosse definitions and interpretations of what those peptidic things are... A peptide is, according to IUPAC gold book https://goldbook.iupac.org/P04479.html: Peptides : Amides<https://goldbook.iupac.org/A00266.html> derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond<https://goldbook.iupac.org/C01384.html> from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. Therefore it includes a combination of all 20 amino acids + all kinds of modifications A peptide is not a peptide ion in the sense of a MS ion as it is usually the charge neutral representation of a combination of a-aminoacids in the case of protein peptides What we represent here are either the molecular ion (peptide sequence represented by one-letter codes + optional PTMs + charged aduct (H+) + charge state) which we can call peptide ion : [ANSpK +2H] 2+ (where Sp is a phosphoserine) which we can interpret with only the sequence with PTMs ANSpK or only with the primary sequence with no PTM ANSK My suggestion then is to keep the term peptide as the most generic and does not need to specify whether it carries PTMs or not: name: peptide-level spectral count # of ANSpK name: sequence-level spectral count # of ANSK name: peptide ion-level spectral count # of [ANSpK+2H]2+ Now if you feel that the term “peptide-level” will be ambiguous (people will not know that peptide sequence and peptide (with or without mods) are different, we can give a clear definition with example or I could recommend using “peptide form level” or “peptide species level” as analogy to protein form or protein species vs protein (top-down inspired definition), but this adds a new definition and make our filkes larger for no good reasons. Pierre-Alain De : Juan Antonio Vizcaino [mailto:ju...@eb...] Envoyé : mercredi 18 janvier 2017 18:23 À : Eric Deutsch Cc : Tobias Ternent; psi...@li...<mailto:psi...@li...>; Robert Chalkley; le...@im...<mailto:le...@im...>; jul...@ru...<mailto:jul...@ru...>; Ghali, Fawaz; mar...@ru...<mailto:mar...@ru...>; mayerg97; Andy Jones; Perkins, Simon; psi...@li...<mailto:psi...@li...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz; Harald Barsnes Objet : Re: [Psidev-pi-dev] mzid 1.2 reviews Fine for me. Sorry, I did not realise about what Eric mentioned. He is completely right. Cheers, Juan On 18 Jan 2017, at 17:18, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: Hi everyone, I agree that splitting this into 3 terms is good. I disagree that we should misuse the term “peptide” and then try to clarify it with a parenthetical expression. I don’t think this is good controlled vocabulary practice. I suspect the true ontology devotees would be horrified by this practice. May I suggest that we use the style that I adopted for the mzIdentML CV reorg? This keeps the term name concise, and we should rely on the definition to remove any ambiguity. I suggest these names instead: name: distinct peptide sequence-level spectral count name: modified peptide sequence-level spectral count name: peptide ion-level spectral count What do you think? Does this capture the desired concepts clearly? Regards, Eric From: Juan Antonio Vizcaino [mailto:ju...@eb...<mailto:ju...@eb...>] Sent: Wednesday, January 18, 2017 1:42 AM To: Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> Cc: mayerg97 <ger...@ru...<mailto:ger...@ru...>>; Andy Jones <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...>; Perkins, Simon <Sim...@li...<mailto:Sim...@li...>>; Harald Barsnes <Har...@ui...<mailto:Har...@ui...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; Tobias Ternent <to...@eb...<mailto:to...@eb...>>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz <eug...@tu...<mailto:eug...@tu...>>; Mathias Walzer <wa...@in...<mailto:wa...@in...>>; Oliver Kohlbacher <oli...@un...<mailto:oli...@un...>>; le...@im...<mailto:le...@im...>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Ghali, Fawaz <F....@li...<mailto:F....@li...>>; Salvador Martínez de Bartolomé <sma...@pr...<mailto:sma...@pr...>>; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi all, I agree with Eric on this. The more clarity the better. What about? [Term] id: MS:1001842 name: peptide PSM count (peptide as the raw peptide sequence) def: "The number of MS2 spectra identified for a given peptide (considering the raw peptide sequence, and merging all charge states, modifications in the same peptide sequence are not considered separately) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence and modifications) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence plus modifications, and merging all charge states) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation [Term] id: MS:1001xxx name: peptide PSM count (peptide as the combination between peptide sequence, modifications and charge state) def: "The number of MS2 spectra identified for a given peptide (considering the peptide sequence and modifications, and one single charge state) in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Of course more variants would need to be created if we would want to mix the definitions above with different charge states, but I think these three definitions would be ok. What happens also in the case of ambiguity in the modification position? So, it could be even more complex. But I think this level is probably ok for the current state of things. Cheers, Juan On 17 Jan 2017, at 15:08, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote: This is pretty good, but I think we should make it completely clear whether it is the number of PSMs per peptide sequence, per peptide with modifications, or per peptide ion (including separate charge states). The plain word peptide is often used as a standin for any of these 3 concepts.. Thanks, Eric From: mayerg97 [mailto:ger...@ru...<mailto:ger...@ru...>] Sent: Tuesday, January 17, 2017 4:39 AM To: Jones, Andy; psi...@li...<mailto:psi...@li...> Cc: Juan Antonio Vizcaino (ju...@eb...<mailto:ju...@eb...>); Perkins, Simon; 'Harald Barsnes'; 'Yasset Perez-Riverol'; to...@eb...<mailto:to...@eb...>; jul...@ru...<mailto:jul...@ru...>; mar...@ru...<mailto:mar...@ru...>; lfi...@st...<mailto:lfi...@st...>; ju...@ed...<mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; Oliver Kohlbacher; le...@im...<mailto:le...@im...>; 'Robert Chalkley'; Ghali, Fawaz; sma...@pr...<mailto:sma...@pr...>; 'Eric Deutsch; psi...@li...<mailto:psi...@li...> Subject: Re: mzid 1.2 reviews Hi Andy, yes we did a CV restructuring, see https://github.com/HUPO-PSI/mzIdentML/issues/25, but I think this problem is not related to the restructuring. What about [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype is_a: MS:1002015 ! spectral count peptide level quantitation Best regards, Gerhard Am 11.01.2017 um 16:56 schrieb Jones, Andy: Hi all, (Sent to PSI-PI mailing list plus authors of the mzid paper, in case any of you are not on the mailing list). We have received 5 reviews of the mzid 1.2 specifications via the PSI process, as well as the 2 reviews received on the manuscript from MCP, for which it makes sense to consider together. I think most of these can be addressed fairly simply. I have already fixed a few typos in the specification document that were identified, and made one or two other sensible clarifications to wording. These changes have been checked into GitHub. I have started response documents to both processes in the relevant zip files. If you would like to contribute, please could you send me any feedback within one week (by 19th Jan) if possible. After that point, I will submit the mzid 1.2 specs back to the PSI process (for which Sylvie the editor recommended minor corrections), unless anything comes up that needs extensive further discussion. Once they are accepted, I will resubmit the paper to MCP, as reporting the mzid 1.2 final specifications. Just flagging a few points for specific people to address: - Robert and Alexander: one of the reviewer asks whether your cross-linking software will export mzid 1.2, anything you can say here? - Fawaz – one of the reviewers seemed to find some validation errors with some of our mzid 1.2 files, please could you take a look - Juan – one of the MCP reviewers suggests we change the figures. Can you give me a view on whether you think we need to do this? I’m of the view to make minor improvements, but not radically change them. - Gerhard – see response to MCP reviews. One of the reviewers would like to know how spectral counts can be added at the peptide-level. I think this may need a new parent term for one given CV term (see my notes in the response to reviews doc), could you take a look? Best wishes Andy -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-vocab mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- -------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER PhD student Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-21006 | Fax +49 (0)234 32-14554 E-mail ger...@ru...<mailto:ger...@ru...> www.medizinisches-proteom-center.de<http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2017-01-26 15:28:53
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Hallo Andy, in that case I would simply propose to add some sub-terms to [Term] id: MS:1001805 name: quantification datatype def: "The data type of the value reported in a QuantLayer for a feature, peptide, protein, protein group." [PSI:MS] is_a: MS:1001129 ! quantification information e.g. [Term] id: MS:1002735 name: feature-level quantification datatype def: "The data type of the value reported in a QuantLayer for a feature." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002736 name: PSM-level quantification datatype def: "The data type of the value reported in a QuantLayer for a PSM." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002737 name: peptide-level quantification datatype def: "The data type of the value reported in a QuantLayer for a peptide." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002738 name: protein-level quantification datatype def: "The data type of the value reported in a QuantLayer for a protein." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002739 name: protein group-level quantification datatype def: "The data type of the value reported in a QuantLayer for a protein group." [PSI:PI] is_a: MS:1001805 ! quantification datatype and to rearrange the current childs of MS:1001805 under these new sub-terms. Would that make sense to you? Best regards, Gerhard Am 26.01.2017 um 10:47 schrieb Jones, Andy: > > Hi Gerhard, > > The part I’m not understanding yet is that we have some CV terms that > are intended to be for peptides in mzid 1.2, meaning a set of grouped > PSMs. Reading software would have to know that they refer to the > grouped peptide concept and not the PSM in which it located them. As > an example: > > [Term] > > id: MS:1002551 > > name: peptide:Ascore > > def: "A-score for PTM site location at the peptide-level." [PSI:PI] > > xref: value-type:xsd\:string "The allowed value-type for this CV term." > > is_a: MS:1002549 ! PTM localization distinct peptide-level statistic > > relationship: has_regexp MS:1002505 ! regular expression for > modification localization scoring > > Which is different from: > > [Term] > > id: MS:1001985 > > name: Ascore > > def: "A-score for PTM site location at the PSM-level." > [DOI:10.1038/nbt1240, PMID:16964243] > > xref: value-type:xsd\:string "The allowed value-type for this CV term." > > is_a: MS:1001968 ! PTM localization PSM-level statistic > > relationship: has_regexp MS:1002505 ! regular expression for > modification localization scoring > > Somewhere higher up in the hierarchy there should be a branch for PSMs > and a branch for peptide level stats or measures. The new terms > proposed need to be within the peptide branch, that’s all I was > suggesting. > > Best wishes > > Andy > > *From:*mayerg97 [mailto:ger...@ru...] > *Sent:* 24 January 2017 11:55 > *To:* psi...@li... > *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews > > Hi Andy, > > yes I think you're right that the parent term 'spectral count peptide > level quantitation' is wrong here, > > since we have the following hierarchy: > > quantitation analysis summary > > spectral counting quantitation analysis > > spectral count peptide level quantitation > > and quantitation analysis summary is defined as "The overall workflow > of this quantitation report." > > > On the other side I don't really understand, why the parent > 'quantification datatype' is > not enough, since by the name of the following three terms it should > be clear that they > are intended as spectral count terms for peptides and not PSM's: > > [Term] > id: MS:1001842 > name: sequence-level spectral count > def: "The number of MS2 spectra identified for a raw peptide sequence > without PTMs and charge state in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > > [Term] > id: MS:1002733 > name: peptide-level spectral count > def: "The number of MS2 spectra identified for a peptide sequence > specified by the amino acid one-letter codes plus optional PTMs in > spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > > [Term] > id: MS:1002734 > name: peptide ion-level spectral count > def: "The number of MS2 spectra identified for a molecular ion defined > by the peptide sequence represented by the amino acid one-letter > codes, plus optional PTMs plus optional charged aducts plus the charge > state, in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > > Best regards, > Gerhard > > Am 20.01.2017 um 12:24 schrieb Jones, Andy: > > Hi Gerhard, > > Thanks for this. Can I check – we want to have these as > peptide-level data types. Can you recall the mapping mechanism > that would tell reading software that these are for peptides > rather than PSMs i.e. they would be repeated for all the PSMs > grouped as the same peptide? The parent terms are not completely > clear to me. > > Best wishes > > Andy > > *From:*mayerg97 [mailto:ger...@ru...] > *Sent:* 20 January 2017 09:41 > *To:* psi...@li... > <mailto:psi...@li...>; > psi...@li... > <mailto:psi...@li...>; > psi...@li... > <mailto:psi...@li...> > *Subject:* Re: [Psidev-ms-vocab] [Psidev-pi-dev] mzid 1.2 reviews > > Hello all, > > so according Pierre-Alains proposal we would have > > [Term] > id: MS:1001842 > name: sequence-level spectral count > def: "The number of MS2 spectra identified for a raw peptide > sequence without PTMs and charge state in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1002733 > name: peptide-level spectral count > def: "The number of MS2 spectra identified for a peptide sequence > specified by the amino acid one-letter codes plus optional PTMs in > spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1002734 > name: peptide ion-level spectral count > def: "The number of MS2 spectra identified for a molecular ion > defined by the peptide sequence represented by the amino acid > one-letter codes, plus optional PTMs plus optional charged aducts > plus the charge state, in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > any futher comments? > > Best regards, > Gerhard > > Am 19.01.2017 um 09:16 schrieb Binz Pierre-Alain: > > Hi all, > > Yep, we are redundantly coming to thosse definitions and > interpretations of what those peptidic things are... > > > A peptide is, according to IUPAC gold book > https://goldbook.iupac.org/P04479.html: > > > Peptides : Amides > <https://goldbook.iupac.org/A00266.html> derived from two or > more amino carboxylic acid molecules (the same or different) > by formation of a covalent bond > <https://goldbook.iupac.org/C01384.html> from the carbonyl > carbon of one to the nitrogen atom of another with formal > loss of water. The term is usually applied to structures > formed from α-amino acids, but it includes those derived > from any amino carboxylic acid. > > Therefore it includes a combination of all 20 amino acids + > all kinds of modifications > > A peptide is not a peptide ion in the sense of a MS ion as it > is usually the charge neutral representation of a combination > of a-aminoacids in the case of protein peptides > > What we represent here are either the molecular ion (peptide > sequence represented by one-letter codes + optional PTMs + > charged aduct (H+) + charge state) which we can call peptide > ion : [ANSpK +2H] 2+ (where Sp is a phosphoserine) which we > can interpret with only the sequence with PTMs ANSpK or > only with the primary sequence with no PTM ANSK > > My suggestion then is to keep the term peptide as the most > generic and does not need to specify whether it carries PTMs > or not: > > name: peptide-level spectral > count # of ANSpK > > name: sequence-level spectral count # of ANSK > > name: peptide ion-level spectral > count # of [ANSpK+2H]2+ > > Now if you feel that the term “peptide-level” will be > ambiguous (people will not know that peptide sequence and > peptide (with or without mods) are different, we can give a > clear definition with example or I could recommend using > “peptide form level” or “peptide species level” as analogy to > protein form or protein species vs protein (top-down inspired > definition), but this adds a new definition and make our > filkes larger for no good reasons. > > Pierre-Alain > > *De :*Juan Antonio Vizcaino [mailto:ju...@eb...] > *Envoyé :* mercredi 18 janvier 2017 18:23 > *À :* Eric Deutsch > *Cc :* Tobias Ternent; psi...@li... > <mailto:psi...@li...>; Robert > Chalkley; le...@im... > <mailto:le...@im...>; > jul...@ru... > <mailto:jul...@ru...>; Ghali, Fawaz; > mar...@ru... <mailto:mar...@ru...>; > mayerg97; Andy Jones; Perkins, Simon; > psi...@li... > <mailto:psi...@li...>; ju...@ed... > <mailto:ju...@ed...>; Eugen Netz; Harald Barsnes > *Objet :* Re: [Psidev-pi-dev] mzid 1.2 reviews > > Fine for me. Sorry, I did not realise about what Eric > mentioned. He is completely right. > > Cheers, > > Juan > > On 18 Jan 2017, at 17:18, Eric Deutsch > <ede...@sy... > <mailto:ede...@sy...>> wrote: > > Hi everyone, I agree that splitting this into 3 terms is > good. I disagree that we should misuse the term “peptide” > and then try to clarify it with a parenthetical > expression. I don’t think this is good controlled > vocabulary practice. I suspect the true ontology devotees > would be horrified by this practice. > > May I suggest that we use the style that I adopted for the > mzIdentML CV reorg? This keeps the term name concise, and > we should rely on the definition to remove any ambiguity. > I suggest these names instead: > > name: distinct peptide sequence-level spectral count > > name: modified peptide sequence-level spectral count > name: peptide ion-level spectral count > > What do you think? Does this capture the desired concepts > clearly? > > Regards, > > Eric > > *From:*Juan Antonio Vizcaino [mailto:ju...@eb... > <mailto:ju...@eb...>] > *Sent:*Wednesday, January 18, 2017 1:42 AM > *To:*Eric Deutsch <ede...@sy... > <mailto:ede...@sy...>> > *Cc:*mayerg97 <ger...@ru... > <mailto:ger...@ru...>>; Andy Jones > <And...@li... > <mailto:And...@li...>>;psi...@li... > <mailto:psi...@li...>; Perkins, > Simon <Sim...@li... > <mailto:Sim...@li...>>; Harald Barsnes > <Har...@ui... <mailto:Har...@ui...>>; > Yasset Perez-Riverol <yp...@eb... > <mailto:yp...@eb...>>; Tobias Ternent > <to...@eb... > <mailto:to...@eb...>>;jul...@ru... > <mailto:jul...@ru...>;mar...@ru... > <mailto:mar...@ru...>;lfi...@st... > <mailto:lfi...@st...>;ju...@ed... > <mailto:ju...@ed...>; Eugen Netz > <eug...@tu... > <mailto:eug...@tu...>>; Mathias Walzer > <wa...@in... > <mailto:wa...@in...>>; Oliver > Kohlbacher <oli...@un... > <mailto:oli...@un...>>;le...@im... > <mailto:le...@im...>; Robert Chalkley > <cha...@cg... <mailto:cha...@cg...>>; > Ghali, Fawaz <F....@li... > <mailto:F....@li...>>; Salvador Martínez de > Bartolomé <sma...@pr... > <mailto:sma...@pr...>>;psi...@li... > <mailto:psi...@li...> > *Subject:*Re: mzid 1.2 reviews > > Hi all, > > I agree with Eric on this. The more clarity the better. > What about? > > [Term] > id: MS:1001842 > name: peptide PSM count (peptide as the raw peptide sequence) > > def: "The number of MS2 spectra identified for a given > peptide (considering the raw peptide sequence, and merging > all charge states, modifications in the same peptide > sequence are not considered separately) in spectral > counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this > CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination > between peptide sequence and modifications) > def: "The number of MS2 spectra identified for a given > peptide (considering the peptide sequence plus > modifications, and merging all charge states) in spectral > counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this > CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > [Term] > id: MS:1001xxx > name: peptide PSM count (peptide as the combination > between peptide sequence, modifications and charge state) > > def: "The number of MS2 spectra identified for a given > peptide (considering the peptide sequence and > modifications, and one single charge state) in spectral > counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for this > CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level quantitation > > Of course more variants would need to be created if we > would want to mix the definitions above with different > charge states, but I think these three definitions would > be ok. > > What happens also in the case of ambiguity in the > modification position? So, it could be even more complex. > But I think this level is probably ok for the current > state of things. > > Cheers, > > Juan > > On 17 Jan 2017, at 15:08, Eric Deutsch > <ede...@sy... > <mailto:ede...@sy...>> wrote: > > This is pretty good, but I think we should make it > completely clear whether it is the number of PSMs per > peptide sequence, per peptide with modifications, or > per peptide ion (including separate charge states). > The plain word peptide is often used as a standin for > any of these 3 concepts.. > > Thanks, > > Eric > > *From:*mayerg97 [mailto:ger...@ru... > <mailto:ger...@ru...>] > *Sent:*Tuesday, January 17, 2017 4:39 AM > *To:*Jones, Andy;psi...@li... > <mailto:psi...@li...> > *Cc:*Juan Antonio Vizcaino (ju...@eb... > <mailto:ju...@eb...>); Perkins, Simon; 'Harald > Barsnes'; 'Yasset Perez-Riverol';to...@eb... > <mailto:to...@eb...>;jul...@ru... > <mailto:jul...@ru...>;mar...@ru... > <mailto:mar...@ru...>;lfi...@st... > <mailto:lfi...@st...>;ju...@ed... > <mailto:ju...@ed...>; Eugen Netz; Mathias Walzer; > Oliver Kohlbacher;le...@im... > <mailto:le...@im...>; 'Robert Chalkley'; > Ghali, Fawaz;sma...@pr... > <mailto:sma...@pr...>; 'Eric > Deutsch;psi...@li... > <mailto:psi...@li...> > *Subject:*Re: mzid 1.2 reviews > > Hi Andy, > > yes we did a CV restructuring, > seehttps://github.com/HUPO-PSI/mzIdentML/issues/25, > but I think this problem is not related to the > restructuring. > > What about > > [Term] > id: MS:1001842 > name: peptide PSM count > def: "The number of MS2 spectra identified for this > peptide in spectral counting." [PSI:PI] > xref: value-type:xsd\:int "The allowed value-type for > this CV term." > is_a: MS:1001805 ! quantification datatype > is_a: MS:1002015 ! spectral count peptide level > quantitation > > Best regards, > Gerhard > > Am 11.01.2017 um 16:56 schrieb Jones, Andy: > > Hi all, > > (Sent to PSI-PI mailing list plus authors of the > mzid paper, in case any of you are not on the > mailing list). > > We have received 5 reviews of the mzid 1.2 > specifications via the PSI process, as well as the > 2 reviews received on the manuscript from MCP, for > which it makes sense to consider together. I think > most of these can be addressed fairly simply. I > have already fixed a few typos in the > specification document that were identified, and > made one or two other sensible clarifications to > wording. These changes have been checked into > GitHub. I have started response documents to both > processes in the relevant zip files. > > *If you would like to contribute, please could you > send me any feedback within one week (by 19^th > Jan) if possible.*After that point, I will submit > the mzid 1.2 specs back to the PSI process (for > which Sylvie the editor recommended minor > corrections), unless anything comes up that needs > extensive further discussion. Once they are > accepted, I will resubmit the paper to MCP, as > reporting the mzid 1.2 final specifications. > > Just flagging a few points for specific people to > address: > > -Robert and Alexander: one of the reviewer asks > whether your cross-linking software will export > mzid 1.2, anything you can say here? > > -Fawaz – one of the reviewers seemed to find some > validation errors with some of our mzid 1.2 files, > please could you take a look > > -Juan – one of the MCP reviewers suggests we > change the figures. Can you give me a view on > whether you think we need to do this? I’m of the > view to make minor improvements, but not radically > change them. > > -Gerhard – see response to MCP reviews. One of the > reviewers would like to know how spectral counts > can be added at the peptide-level. I think this > may need a new parent term for one given CV term > (see my notes in the response to reviews doc), > could you take a look? > > Best wishes > > Andy > > -- > > *--------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building*ZKF E.049a|Universitätsstraße 150 | D-44801 > Bochum > > *Fon*+49 (0)234 32-21006|*Fax*+49 (0)234 32-14554 > > *E-mail*ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de/> > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org!http://sdm.link/slashdot > > > > > > _______________________________________________ > > Psidev-ms-vocab mailing list > > Psi...@li... > <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab > > -- > > *--------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail *ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de/> > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org!http://sdm.link/slashdot > > > > > _______________________________________________ > > Psidev-ms-vocab mailing list > > Psi...@li... > <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab > > -- > > *--------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 > > *E-mail *ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de/> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-ms-vocab mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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