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Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2
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From: Jones, A. <And...@li...> - 2016-04-04 08:40:46
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Hi Matthias, Thanks for your comments, answers in line: -----Original Message----- From: Mathias Walzer [mailto:wa...@in...] Sent: 31 March 2016 16:57 To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2 Hi all, I feel a little silly, seems I was not able to dial in (enter access code does not work) - the institute's telephone system was switched, I guess it does not support this kind of function anymore. Anyways, maybe just some points in brief. mzid schema general issues: why is experimental m/z in not in SpectrumIdentificationResult but (repeatedly) in SpectrumIdentificationItem? Why is peptide_ref in SpectrumIdentificationItem optional? As are the PeptideEvidence elements. Because of the potential small molecule usecase? >> You are correct that "experimental m/z" should be an attribute of SpectrumIdentificationResult - this was an error in mzid 1.1. I hadn't considered changing it, since we are trying to make mzid 1.2 as near as backwards compatible as possible. Any opinions as to whether this is worth changing? Why is peptide_ref in SpectrumIdentificationItem optional? >>I don't know why we ever did this in mzid 1.1, possibly a mistake or a use case we never fully explored. I would vote for making it mandatory now in mzid 1.2, as we are revisiting cardinality and optionality of elements/attributes. Opinions all? >> As are the PeptideEvidence elements. This is to account for de novo sequencing and spectral library approaches, where peptides may not be linked to a parent protein. In a regular sequence database search, the validator checks that they are always present. mzid ppxl issues: we will need many more CV entries. E.g. the types of cross-link. Be it a mono-link, loop-link or cross-link. >> Please suggest terms needed and we will add them. And there are only mono-link definitions in unimod (and only for DSS), so I guess we need more reagents used for crosslinking in one of the ontologies that define the pairs, >> Lutz is working on a list of reagent CV terms to be added to PSI-MS CV, please coordinate with him. Also, to my understanding, isotope labeling is often used as a measure of reassurance of the identified cross-links. I suppose that kind of detected pairing information would go in the SpectrumIdentificationResult? >> Good point, although we haven't got a formal way of doing this. Scores can obviously be added but we don't have a way of formally linking differentially labelled pairs (nor for regular SILAC either though). This might be considered out of scope in mzIdentML, but please send a suggestion for how the data looks from a search engine. And there seems to be ambiguous definition available on the pairing of the different SpectrumIdentificationItem elements in one SpectrumIdentificationResult as linked peptides. It is the value of cv term 'cross-link spectrum identification item', isn't it - so we can use rank for sorting? >> The value of 'cross-link spectrum identification item' is a local unique identifier tying together the crosslinked peptides. Do you think this is still ambiguous? Best wishes Andy best, Mathias ----- Original Message ----- From: "Andy Jones" <And...@li...> To: psi...@li... Cc: psi...@li... Sent: Thursday, 31 March, 2016 4:45:07 PM Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2 Dial-in details, call in 15 mins: Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy [mailto:And...@li...] Sent: 29 March 2016 16:10 To: psi...@li... Cc: psi...@li... Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, Just confirming we will have a call to discuss mzid 1.2 this coming Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 Agenda: 1. Discussion of encoding proteogenomics results in mzid 1.2 (review of docs sent previously) 2. General review of mzid 1.2 specifications (attached here) – please take a look in advance if you can. We will probably not have time for a full review on the call, but we will see how far we get 3. Any other business Juan – are you okay to start the call, and if so, can you circulate dial-in details? Thanks Andy From: Binz Pierre-Alain [ mailto:Pie...@ch... ] Sent: 22 March 2016 15:45 To: psi...@li... Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Fine for me too Pierre-Alain De : Eric Deutsch [ mailto:ede...@sy... ] Envoyé : mardi 22 mars 2016 14:53 À : psi...@li... ; Mass spectrometry standard development; psi...@li... Objet : Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 That works fine for me! From: Jones, Andy [mailto: And...@li... ] Sent: Tuesday, March 22, 2016 2:49 AM To: Mass spectrometry standard development; psi...@li... ; psi...@li... Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, I think the 24 th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing. On the 31 st , my preferred slot is actually 4pm British summer time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 This would be 8am in Seattle; 5pm Germany; 5pm Norway; (and 4pm in the independent nation state of the EBI) Does this work for everyone? Best wishes Andy From: Eric Deutsch [ mailto:ede...@sy... ] Sent: 22 March 2016 03:32 To: Mass spectrometry standard development < psi...@li... >; psi...@li... ; psi...@li... Cc: Eric Deutsch < ede...@sy... > Subject: Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change. http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440 An hour earlier would be fine for the 24 th . I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24 th 16:00 GMT = 4pm local London, but on the 31 st , 16:00 GMT is 5pm London time? Thanks, Eric From: Jones, Andy [mailto: And...@li... ] Sent: Monday, March 21, 2016 4:21 AM To: psi...@li... ; psi...@li... ; psi...@li... Subject: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list. One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches. There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides). Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion. It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit: - This Thurs (24 th March) at 4pm GMT - Next Thurs (31 st March) at 4pm GMT Best wishes Andy ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. 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