psidev-qc-dev — PSI-QC working group mailinglist

[Psidev-qc-dev] Upcoming teleconference 11/8

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 11, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   One major item! Integration of the QC CV with the MS CV. Feedback from the PSI steering committee on the specification document is that we should try to harmonize and/or integrate both CVs. What are potential issues hindering this and how can we solve them?

Best,
Wout

[Psidev-qc-dev] NO teleconference 28/7

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

Due to vacations and engagements in the ISMB/ECCB conference that is currently ongoing, we will not have a meeting tomorrow, Wednesday July 27.

As discussed during our previous meeting, due to the summer break we will have only meetings in August if enough people are able to attend. Please fill out the following Doodle to indicate your availability: https://doodle.com/poll/4nym9y6wf39ibek8<https://doodle.com/poll/4nym9y6wf39ibek8?utm_source=poll&utm_medium=link>

Thanks,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 14/7

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/2021/20210714_telco.md

The main point is that Mathias & I will finish the response to the reviewers this week and resubmit the specification document for public review.

Considering that multiple people will be on holiday at various points during the next few weeks, we are considering to have a short teleconference break. Please communicate when you can/cannot attend our bi-weekly meetings.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, July 13, 2021 17:24
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 14/7

Dear colleagues,

We have our next teleconference tomorrow, Wednesday July 14, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Finish specification document response to reviewers<https://docs.google.com/document/d/14mC7sDjPpeg7uFVZSaPv799CgSHqKMmzKuv-rLepuhc/edit?usp=sharing>

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 14/7

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday July 14, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Finish specification document response to reviewers<https://docs.google.com/document/d/14mC7sDjPpeg7uFVZSaPv799CgSHqKMmzKuv-rLepuhc/edit?usp=sharing>

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 30/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find today's meeting notes here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/2021/20210630_telco.md

Please take note of the following two deadlines:

  *   Provide feedback on the ASMS workshop proposal<https://docs.google.com/document/d/10-ZY-hiIZqlcKjsgyarlRUF2MN7GuTWJJlaV3MQjcMY/edit?usp=sharing> by July 1.
  *   Contribute to the specification document response to reviewers<https://docs.google.com/document/d/14mC7sDjPpeg7uFVZSaPv799CgSHqKMmzKuv-rLepuhc/edit> by July 13.

Best,
Wout

________________________________
From: Bittremieux, Wout
Sent: Tuesday, June 29, 2021 19:05
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 30/6

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 30, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!yYUHHpxOYxQ5Wvwp5LsSprzI6SQfPMUY0f8FQU5LFxbi7FRtezqlpDtMHU-8Td0RDuHPkg$>
(Password: 012575)

Agenda items:

  *   ASMS workshop application: instructions here<https://applications-and-award-nominations.formstack.com/forms/asms_workshop_independent_2021>, draft abstract here<https://docs.google.com/document/d/10-ZY-hiIZqlcKjsgyarlRUF2MN7GuTWJJlaV3MQjcMY/edit?usp=sharing> (deadline July 1!)
  *   Specification document response to reviewers (Mathias status update)
  *   Time permitting: Start addressing open issues and PRs on GitHub

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 30/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 30, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!yYUHHpxOYxQ5Wvwp5LsSprzI6SQfPMUY0f8FQU5LFxbi7FRtezqlpDtMHU-8Td0RDuHPkg$>
(Password: 012575)

Agenda items:

  *   ASMS workshop application: instructions here<https://applications-and-award-nominations.formstack.com/forms/asms_workshop_independent_2021>, draft abstract here<https://docs.google.com/document/d/10-ZY-hiIZqlcKjsgyarlRUF2MN7GuTWJJlaV3MQjcMY/edit?usp=sharing> (deadline July 1!)
  *   Specification document response to reviewers (Mathias status update)
  *   Time permitting: Start addressing open issues and PRs on GitHub

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 16/6

[David T. <dav...@pa...>]

Excellent work, everyone!

I am very proud to work with such diligent researchers!

Thanks,
Dave

From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Friday, June 18, 2021 12:35 AM
To: psi...@li...
Subject: Re: [Psidev-qc-dev] Upcoming teleconference 16/6

Dear colleagues,

You can find the meeting notes of yesterday's call here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210616_telco.md<https://urldefense.com/v3/__https:/github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210616_telco.md__;!!JFdNOqOXpB6UZW0!7xWa1xpde_Q9Dfo5OzQz2BYAxdODJxiv85q10v0HTy6JxWFQYbXh0dE6KwLsIKQ$>

The specification document is now final. Mathias will share a Google Doc to draft a response to reviewers, after which the specification document will be resubmitted for review.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, June 15, 2021 21:05
To: psi...@li...<mailto:psi...@li...> <psi...@li...<mailto:psi...@li...>>
Subject: Upcoming teleconference 16/6

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 16, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

We have one big task for tomorrow:

  *   Final meeting to discuss the specification document before public review!

     *   Units of tabular metrics (see previous email discussion).
     *   Last chance to give comments.
Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 16/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of yesterday's call here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210616_telco.md

The specification document is now final. Mathias will share a Google Doc to draft a response to reviewers, after which the specification document will be resubmitted for review.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, June 15, 2021 21:05
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 16/6

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 16, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

We have one big task for tomorrow:

  *   Final meeting to discuss the specification document before public review!
     *   Units of tabular metrics (see previous email discussion).
     *   Last chance to give comments.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 16/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 16, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

We have one big task for tomorrow:

  *   Final meeting to discuss the specification document before public review!
     *   Units of tabular metrics (see previous email discussion).
     *   Last chance to give comments.

Best,
Wout

Re: [Psidev-qc-dev] QuaMeter ID-free mzQC example

[Julian U. <jul...@ru...>]

Hej Wout,

Hm, I guess the only reason, why we introduced the "Fraction 
(QC:4000239)" is, that it is also a "is_a: QC:4000107 ! Column type". 
This is (should be!) mandatory for the column and, at least to my 
knowledge, you can only assign the types we created in the CV right now.

I am not too sure whether this should be the way to go, maybe discuss it 
in the next telco?

Best,
Julian


On 09.06.21 15:41, Bittremieux, Wout via Psidev-qc-dev wrote:
> Yes, as far as I read the spec both versions are compliant, as units for 
> table metrics don't really seem unambiguously described currently. 
> Possibly an oversight because we didn't have a proper example of this 
> yet? I think the second version is more in line with units for other 
> metric types though and is more descriptive. We'll need to properly 
> include this in the spec then.
> 
> One other comment is that I now used terms from the Unit Ontology as 
> units. There are also terms in our QC-CV that are the same except that 
> they're wrappers for those units to be used as table columns. See for 
> example "fraction (UO:0000191) 
> <https://github.com/bio-ontology-research-group/unit-ontology/blob/master/unit.obo#L2469>" 
> vs "Fraction (QC:4000239) 
> <https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo#L1884>". I 
> have forgotten the previous discussion about this. What is the advantage 
> of introducing new CV terms for these units? *@Julian* maybe? To be able 
> to do a semantic check that these explicitly are column headers? I don't 
> really see a strong reason to have to duplicate CV terms when used as 
> column labels.
> 
> Best,
> Wout
> ------------------------------------------------------------------------
> *From:* David TABB <dav...@pa...>
> *Sent:* Wednesday, June 9, 2021 4:32
> *To:* Bittremieux, Wout <wbi...@he...>
> *Subject:* RE: QuaMeter ID-free mzQC example
> 
> Hi, Wout.  Very nice work!
> 
> The XIC-FWHM values are peak widths, measured in seconds.
> 
> Ratio rather than log ratio will be fine, since that’s what we have 
> available.  Of course, a 1:1 ratio is 1.0 in linear space rather than 
> 0.0 in log space, but c’est la vie.
> 
> I think of the precursor charge states as being a “proportion,” where 
> the sum of all equals 1.0 rather than a “percentage,” where the sum is 
> 100%, or a “fraction,” where the sum is arbitrary.  I think that level 
> of nuance is unnecessary to resolve for this example, though.
> 
> I like the variation where you include the unit types for each column in 
> the trailer, but do both of these formattings comply with the spec as 
> written?
> 
> Thank you,
> 
> Dave
> 
> *From:* Bittremieux, Wout via Psidev-qc-dev 
> <psi...@li...>
> *Sent:* Wednesday, June 9, 2021 2:31 AM
> *To:* psi...@li...
> *Subject:* [Psidev-qc-dev] QuaMeter ID-free mzQC example
> 
> Dear colleagues,
> 
> I have updated the mzQC example with QuaMeter ID-free metrics here: 
> https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725 
> <https://urldefense.com/v3/__https:/gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725__;!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWamNToUEQ$>
> 
> Please check it out and provide any feedback.
> 
> I had a few open questions:
> 
>   * @Dave: I'm still missing the unit for metric "XIC-FWHM quantiles"
>     <https://urldefense.com/v3/__https:/github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo*L212__;Iw!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWaQKpTz5s$>.
>     What would be the correct unit there?
>   * Some of the metric values are "log ratios". I have now used "ratio"
>     as unit for these metrics because I couldn't find a log ratio term
>     in the Unit Ontology. Is this correct?
>   * Please have a look at the table metrics "MS2 known precursor charges
>     fractions" and "MS2 unknown and likely precursor charges fractions".
>     The column headers are terms from the Unit Ontology ("Charge state"
>     and "Fraction"), as also described in the specification document in
>     section 4.1.1 on page 11 ("table column type definitions"). This
>     defines the unit of the table's columns, as specified, but by not
>     explicitly including the term's accession and only using the name,
>     the link to a controlled vocabulary is lost in the mzQC file. Should
>     we maybe repeat the units for tables as a "unit" element as well?
>     For example, current:
> 
> {
> 
>      "accession": "QC:4000063",
> 
>      "name": "MS2 known precursor charges fractions",
> 
>      "value": {
> 
>          "Charge state": [
> 
>          "1",
> 
>          "2",
> 
>          "3",
> 
>          "4",
> 
>          "5",
> 
>          "6"
> 
>          ],
> 
>          "Fraction": [
> 
>          0,
> 
>          0.6830609999999999,
> 
>          0.305012,
> 
>          0.00844278,
> 
>          0.00134012,
> 
>          0.0021441999999999998
> 
>          ]
> 
>      }
> 
> }
> 
> Alternative:
> 
> {
> 
>      "accession": "QC:4000063",
> 
>      "name": "MS2 known precursor charges fractions",
> 
>      "value": {
> 
>          "Charge state": [
> 
>          "1",
> 
>          "2",
> 
>          "3",
> 
>          "4",
> 
>          "5",
> 
>          "6"
> 
>          ],
> 
>          "Fraction": [
> 
>          0,
> 
>          0.6830609999999999,
> 
>          0.305012,
> 
>          0.00844278,
> 
>          0.00134012,
> 
>          0.0021441999999999998
> 
>          ]
> 
>      },
> 
>      "unit": [
> 
>          {
> 
>              "accession": "MS:1000041",
> 
>              "name": "charge state"
> 
>          },
> 
>          {
> 
>              "accession": "UO:0000191",
> 
>              "name": "fraction"
> 
>          }
> 
>      ]
> 
> }
> 
> 	
> 	
> 
> Maybe the latter was our intention already, because "unit" is allowed to 
> be an array according to the JSON Schema and specification document. If 
> so, we should clarify in the specification document how table units 
> should be a list that matches the column order.
> 
> Thank you for having a look at these questions.
> 
> Best,
> 
> Wout
> 
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
> 

Re: [Psidev-qc-dev] QuaMeter ID-free mzQC example

[Bittremieux, W. <wbi...@he...>]

Yes, as far as I read the spec both versions are compliant, as units for table metrics don't really seem unambiguously described currently. Possibly an oversight because we didn't have a proper example of this yet? I think the second version is more in line with units for other metric types though and is more descriptive. We'll need to properly include this in the spec then.

One other comment is that I now used terms from the Unit Ontology as units. There are also terms in our QC-CV that are the same except that they're wrappers for those units to be used as table columns. See for example "fraction (UO:0000191)<https://github.com/bio-ontology-research-group/unit-ontology/blob/master/unit.obo#L2469>" vs "Fraction (QC:4000239)<https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo#L1884>". I have forgotten the previous discussion about this. What is the advantage of introducing new CV terms for these units? @Julian maybe? To be able to do a semantic check that these explicitly are column headers? I don't really see a strong reason to have to duplicate CV terms when used as column labels.

Best,
Wout
________________________________
From: David TABB <dav...@pa...>
Sent: Wednesday, June 9, 2021 4:32
To: Bittremieux, Wout <wbi...@he...>
Subject: RE: QuaMeter ID-free mzQC example


Hi, Wout.  Very nice work!



The XIC-FWHM values are peak widths, measured in seconds.



Ratio rather than log ratio will be fine, since that’s what we have available.  Of course, a 1:1 ratio is 1.0 in linear space rather than 0.0 in log space, but c’est la vie.



I think of the precursor charge states as being a “proportion,” where the sum of all equals 1.0 rather than a “percentage,” where the sum is 100%, or a “fraction,” where the sum is arbitrary.  I think that level of nuance is unnecessary to resolve for this example, though.



I like the variation where you include the unit types for each column in the trailer, but do both of these formattings comply with the spec as written?



Thank you,

Dave



From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, June 9, 2021 2:31 AM
To: psi...@li...
Subject: [Psidev-qc-dev] QuaMeter ID-free mzQC example



Dear colleagues,



I have updated the mzQC example with QuaMeter ID-free metrics here: https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725<https://urldefense.com/v3/__https:/gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725__;!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWamNToUEQ$>



Please check it out and provide any feedback.



I had a few open questions:

  *   @Dave: I'm still missing the unit for metric "XIC-FWHM quantiles"<https://urldefense.com/v3/__https:/github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo*L212__;Iw!!JFdNOqOXpB6UZW0!_5wyaFE5AqXlNGS7vHPlkoz7VZM5nQpv_sePdYjmUqyoFjOH98anwTWaQKpTz5s$>. What would be the correct unit there?
  *   Some of the metric values are "log ratios". I have now used "ratio" as unit for these metrics because I couldn't find a log ratio term in the Unit Ontology. Is this correct?
  *   Please have a look at the table metrics "MS2 known precursor charges fractions" and "MS2 unknown and likely precursor charges fractions". The column headers are terms from the Unit Ontology ("Charge state" and "Fraction"), as also described in the specification document in section 4.1.1 on page 11 ("table column type definitions"). This defines the unit of the table's columns, as specified, but by not explicitly including the term's accession and only using the name, the link to a controlled vocabulary is lost in the mzQC file. Should we maybe repeat the units for tables as a "unit" element as well? For example, current:

{

    "accession": "QC:4000063",

    "name": "MS2 known precursor charges fractions",

    "value": {

        "Charge state": [

        "1",

        "2",

        "3",

        "4",

        "5",

        "6"

        ],

        "Fraction": [

        0,

        0.6830609999999999,

        0.305012,

        0.00844278,

        0.00134012,

        0.0021441999999999998

        ]

    }

}

Alternative:



{

    "accession": "QC:4000063",

    "name": "MS2 known precursor charges fractions",

    "value": {

        "Charge state": [

        "1",

        "2",

        "3",

        "4",

        "5",

        "6"

        ],

        "Fraction": [

        0,

        0.6830609999999999,

        0.305012,

        0.00844278,

        0.00134012,

        0.0021441999999999998

        ]

    },

    "unit": [

        {

            "accession": "MS:1000041",

            "name": "charge state"

        },

        {

            "accession": "UO:0000191",

            "name": "fraction"

        }

    ]

}



Maybe the latter was our intention already, because "unit" is allowed to be an array according to the JSON Schema and specification document. If so, we should clarify in the specification document how table units should be a list that matches the column order.



Thank you for having a look at these questions.



Best,

Wout

[Psidev-qc-dev] QuaMeter ID-free mzQC example

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

I have updated the mzQC example with QuaMeter ID-free metrics here: https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725

Please check it out and provide any feedback.

I had a few open questions:

  *   @Dave: I'm still missing the unit for metric "XIC-FWHM quantiles"<https://github.com/HUPO-PSI/mzQC/blob/master/cv/qc-cv.obo#L212>. What would be the correct unit there?
  *   Some of the metric values are "log ratios". I have now used "ratio" as unit for these metrics because I couldn't find a log ratio term in the Unit Ontology. Is this correct?
  *   Please have a look at the table metrics "MS2 known precursor charges fractions" and "MS2 unknown and likely precursor charges fractions". The column headers are terms from the Unit Ontology ("Charge state" and "Fraction"), as also described in the specification document in section 4.1.1 on page 11 ("table column type definitions"). This defines the unit of the table's columns, as specified, but by not explicitly including the term's accession and only using the name, the link to a controlled vocabulary is lost in the mzQC file. Should we maybe repeat the units for tables as a "unit" element as well? For example, current:

{
    "accession": "QC:4000063",
    "name": "MS2 known precursor charges fractions",
    "value": {
        "Charge state": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6"
        ],
        "Fraction": [
        0,
        0.6830609999999999,
        0.305012,
        0.00844278,
        0.00134012,
        0.0021441999999999998
        ]
    }
}

Alternative:

{
    "accession": "QC:4000063",
    "name": "MS2 known precursor charges fractions",
    "value": {
        "Charge state": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6"
        ],
        "Fraction": [
        0,
        0.6830609999999999,
        0.305012,
        0.00844278,
        0.00134012,
        0.0021441999999999998
        ]
    },
    "unit": [
        {
            "accession": "MS:1000041",
            "name": "charge state"
        },
        {
            "accession": "UO:0000191",
            "name": "fraction"
        }
    ]
}


Maybe the latter was our intention already, because "unit" is allowed to be an array according to the JSON Schema and specification document. If so, we should clarify in the specification document how table units should be a list that matches the column order.

Thank you for having a look at these questions.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 2/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of yesterday's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210602_telco.md

Please note the following schedule for finalization of the specification document:

  *   Until Wednesday June 9, 2021: Mathias, Wout, Dave finalize the specification document and do final checks.
  *   Until Wednesday June 16, 2021 (next teleconference): Send the specification document to the QC mailing list and everyone gives final feedback!

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, June 1, 2021 19:45
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 2/6

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 2, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- To ASMS workshop or not to ASMS workshop? Apply here<https://applications-and-award-nominations.formstack.com/forms/asms_workshop_independent_2021> by July 1.
- Specification document updates (Mathias): Sections 5.1 (mzML) & 5.4 (USI), related issue 130<https://github.com/HUPO-PSI/mzQC/issues/130>.
- Examples
    - Combination of mzML and mzQC (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>; section 5.1)
    - nativeID and USI (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>; section 5.4)
    - setQuality (PR 112<https://github.com/HUPO-PSI/mzQC/pull/112>)
    - QuaMeter (issue 11<https://github.com/HUPO-PSI/mzQC/issues/11>; mzQC example<https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725>)
    - mzTab (section 5.3)
    - SDRF (section 5.5)
- Semantic/syntactic validation (issue 51<https://github.com/HUPO-PSI/mzQC/issues/51>, mzqc-pylib<https://github.com/bigbio/mzqc-pylib>, specification document section 8).
    - mzqc-pylib code style

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 2/6

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday June 2, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- To ASMS workshop or not to ASMS workshop? Apply here<https://applications-and-award-nominations.formstack.com/forms/asms_workshop_independent_2021> by July 1.
- Specification document updates (Mathias): Sections 5.1 (mzML) & 5.4 (USI), related issue 130<https://github.com/HUPO-PSI/mzQC/issues/130>.
- Examples
    - Combination of mzML and mzQC (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>; section 5.1)
    - nativeID and USI (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>; section 5.4)
    - setQuality (PR 112<https://github.com/HUPO-PSI/mzQC/pull/112>)
    - QuaMeter (issue 11<https://github.com/HUPO-PSI/mzQC/issues/11>; mzQC example<https://gist.github.com/bittremieux/a3a43ce929e38fd0230005782f3c9725>)
    - mzTab (section 5.3)
    - SDRF (section 5.5)
- Semantic/syntactic validation (issue 51<https://github.com/HUPO-PSI/mzQC/issues/51>, mzqc-pylib<https://github.com/bigbio/mzqc-pylib>, specification document section 8).
    - mzqc-pylib code style

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 19/5

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of today's teleconference here<https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210519_telco.md>.

Notably, we decided not to add a userParameter element.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, May 18, 2021 18:04
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 19/5

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 19, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- Finalize userParameter (issue 126<https://github.com/HUPO-PSI/mzQC/issues/126> & PR 128<https://github.com/HUPO-PSI/mzQC/pull/128>).
- Examples: combination of mzML and mzQC (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>), nativeID and USI (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>), setQuality (PR 112<https://github.com/HUPO-PSI/mzQC/pull/112>), QuaMeter (issue 11<https://github.com/HUPO-PSI/mzQC/issues/11>), mzTab, SDRF.
- Semantic/syntactic validation (issue 51<https://github.com/HUPO-PSI/mzQC/issues/51>, mzqc-pylib<https://github.com/bigbio/mzqc-pylib>, specification document section 8).

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 19/5

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 19, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- Finalize userParameter (issue 126<https://github.com/HUPO-PSI/mzQC/issues/126> & PR 128<https://github.com/HUPO-PSI/mzQC/pull/128>).
- Examples: combination of mzML and mzQC (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>), nativeID and USI (issue 56<https://github.com/HUPO-PSI/mzQC/issues/56>), setQuality (PR 112<https://github.com/HUPO-PSI/mzQC/pull/112>), QuaMeter (issue 11<https://github.com/HUPO-PSI/mzQC/issues/11>), mzTab, SDRF.
- Semantic/syntactic validation (issue 51<https://github.com/HUPO-PSI/mzQC/issues/51>, mzqc-pylib<https://github.com/bigbio/mzqc-pylib>, specification document section 8).

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 5/5

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

Please find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20210505_telco.md

I would especially like to ask everyone to have a look at issue 126<https://github.com/HUPO-PSI/mzQC/issues/126> and PR 128<https://github.com/HUPO-PSI/mzQC/pull/128> about whether we should add a userParameter element to allow metrics that don't have a CV term, as requested by the reviewers. Because this is an important issue that has to be decided to finalize the specification document, I would like to ask everyone to weigh in and help resolve this issue before our next call in two weeks. Based on the group's consensus I will then update the specification document accordingly.

Thank you,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, May 4, 2021 17:32
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 5/5

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 5, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09 (Password: 012575)

Agenda items:

Action points from the last call:

✔️ Section 9.3: Specify how non-computable numbers (NaN, Inf) should be encoded.
✔️ Section 4.1: Add a brief introduction to OBO and OBO Foundry.
✔️ Section 4.1: Specify that the MS CV and QC CV are developed in parallel (but not planned to be merged).
✔️ Section 4.1.1: Refer to the GitHub issue tracker to request new CV terms.
- @julian: Figure out how we can submit the CV to the Ontology Lookup Service.
- Mention that an mzML file may report that a corresponding mzQC file has been developed that incorporates it. Create a small mzML–mzQC example file on GitHub.
- Include examples with both nativeID and USI specifiers.
✔️ Section 5.3: Mention directly including metrics in an mzTab file.
✔️ Section 5.5: SDRF can help to define the study design to inform the calculation of QC metrics.
✔️ PR 128: Provide a userParam type for temporary metrics that don't have a CV term (yet). Please review!
✔️ Specify the type of arrays by replacing "array" by "array of TYPE".
- @mwalzer: Address syntactic and semantic validation of mzQC files.
✔️ @wout: Change to a CC BY-NC license.

Depending on whether we have more time:

- Evaluate examples on GitHub. Which examples are still missing and do we need more?
- Semantic validation (see Slack and issue 51).

Please communicate other agenda items to the mailing list.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 5/5

[David T. <dav...@pa...>]

Hi, all.

This afternoon I am teaching essentials of proteome informatics to the local Ph.D. students, so I will not be able to chair.  Mathias, could you manage finalizing our last details?  I want to finalize the spec at the earliest opportunity.

Thanks,
Dave

From: Bittremieux, Wout via Psidev-qc-dev <psi...@li...>
Sent: Wednesday, May 5, 2021 2:32 AM
To: psi...@li...
Subject: [Psidev-qc-dev] Upcoming teleconference 5/5

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 5, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09 (Password: 012575)

Agenda items:

Action points from the last call:

✔️ Section 9.3: Specify how non-computable numbers (NaN, Inf) should be encoded.
✔️ Section 4.1: Add a brief introduction to OBO and OBO Foundry.
✔️ Section 4.1: Specify that the MS CV and QC CV are developed in parallel (but not planned to be merged).
✔️ Section 4.1.1: Refer to the GitHub issue tracker to request new CV terms.
- @julian: Figure out how we can submit the CV to the Ontology Lookup Service.
- Mention that an mzML file may report that a corresponding mzQC file has been developed that incorporates it. Create a small mzML–mzQC example file on GitHub.
- Include examples with both nativeID and USI specifiers.
✔️ Section 5.3: Mention directly including metrics in an mzTab file.
✔️ Section 5.5: SDRF can help to define the study design to inform the calculation of QC metrics.
✔️ PR 128: Provide a userParam type for temporary metrics that don't have a CV term (yet). Please review!
✔️ Specify the type of arrays by replacing "array" by "array of TYPE".
- @mwalzer: Address syntactic and semantic validation of mzQC files.
✔️ @wout: Change to a CC BY-NC license.

Depending on whether we have more time:

- Evaluate examples on GitHub. Which examples are still missing and do we need more?
- Semantic validation (see Slack and issue 51).

Please communicate other agenda items to the mailing list.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 5/5

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday May 5, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09 (Password: 012575)

Agenda items:

Action points from the last call:

✔️ Section 9.3: Specify how non-computable numbers (NaN, Inf) should be encoded.
✔️ Section 4.1: Add a brief introduction to OBO and OBO Foundry.
✔️ Section 4.1: Specify that the MS CV and QC CV are developed in parallel (but not planned to be merged).
✔️ Section 4.1.1: Refer to the GitHub issue tracker to request new CV terms.
- @julian: Figure out how we can submit the CV to the Ontology Lookup Service.
- Mention that an mzML file may report that a corresponding mzQC file has been developed that incorporates it. Create a small mzML–mzQC example file on GitHub.
- Include examples with both nativeID and USI specifiers.
✔️ Section 5.3: Mention directly including metrics in an mzTab file.
✔️ Section 5.5: SDRF can help to define the study design to inform the calculation of QC metrics.
✔️ PR 128: Provide a userParam type for temporary metrics that don't have a CV term (yet). Please review!
✔️ Specify the type of arrays by replacing "array" by "array of TYPE".
- @mwalzer: Address syntactic and semantic validation of mzQC files.
✔️ @wout: Change to a CC BY-NC license.

Depending on whether we have more time:

- Evaluate examples on GitHub. Which examples are still missing and do we need more?
- Semantic validation (see Slack and issue 51).

Please communicate other agenda items to the mailing list.

Best,
Wout

[Psidev-qc-dev] HUPO PSI specification: MAGETAB and SDRF for Proteomics - 60-day public review

[Sylvie R. <syl...@un...>]

Dear colleague, dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of PSI activities).

The PSI Mass Spectrometry and Proteomics Informatics Working Groups have 
submitted to the PSI document process a document presenting a 
specification for a sample metadata annotation of proteomics 
experiments. The document is entitled “MAGE-TAB Proteomics: Sample and 
Data Relationship Format (SDRF) for Proteomics” version 1.0.
After having passed a 30-day review of the PSI steering group and being 
revised, the proposed document now goes through 60-day public comments 
and external review phase until June 30, 2021.

- The .docx file " is attached to this e-mail.
- Further detailed information, including any updates to this document, 
implementations, and examples is available at 
https://github.com/bigbio/proteomics-metadata-standard.
- The PSI web page for the document is 
https://www.psidev.info/magetab-and-sdrf-proteomics

This message is to encourage you to contribute to the standards 
development activity by commenting on the document. We invite both 
positive and negative comments on the relevance, correctness, clarity 
and appropriateness of the specification (e.g. is it presented in 
accordance with the templates and clearly written, is it sufficiently 
detailed and comprehensively described and are the examples in agreement 
with the specification?). Comments can be made on the specification as a 
whole or on specific parts.

If you do not feel experienced enough to comment on this document, but 
know colleagues who are, please feel free to forward this message to 
them. There is no requirement that people commenting should have had any 
prior contact with the PSI.

*Please send comments by e-mail directly to 
syl...@un... before June 30, 2021.*

Thank you very much in advance for your valuable help.

Kind regards.

Professor Sylvie RICARD-BLUM, *HUPO-PSI Editor*
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...

[Psidev-qc-dev] Upcoming teleconference 21/04

[Wout B. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday April 21, at 14h00
GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification
document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the
following link:
https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- Finalize the specification document
(https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit).
- CV update: newly requested terms (PR #125), browsing (issue #119), 
hierarchy (issue #120).
- Define rules for semantic validation (see Slack for items identified 
during the previous call).

Please communicate other agenda items to the mailing list.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 07/04

[Wout B. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday April 7, at 14h00 
GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

Note that we have decided to meet bi-weekly to finish the specification 
document and manuscript(s) discussed during the Spring Meeting.

You can connect to our teleconference on Zoom through the
following link: 
https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

- **Finish** the specification document 
(https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit). 
To do so, I would like to ask that you check the document prior to the 
meeting and try to resolve any open issues you feel can be easily resolved.
- Update of the working group's page on the PSI website 
(https://psidev.info/groups/quality-control).

Please communicate other agenda items to the mailing list.

Best,
Wout

[Psidev-qc-dev] PSI-QC webpage

[David T. <dav...@pa...>]

Hi, folks.  I really enjoyed talking with you at the HUPO-PSI spring meeting!

The steering committee is trying to ensure that the websites for individual work groups are still up-to-date.  In looking at ours (https://www.psidev.info/groups/quality-control), I have the following comments and suggestions:

  1.  "View Documents" at the top points to the PSI file collection rather than our GitHub.
  2.  Under "Focus and Purpose" we specify that we have industry researchers, journal representatives, and instrument manufacturers represented in our team.  Has that ever been true?
  3.  The "Current Projects" section specifies our development of qcML (sic).  Similarly our second though sixth points in "Goals/Milestones" specify development of qcML.
  4.  Stefan Tenzer is listed as a co-chair, but I think it has been more than a year since our last contact, yes?
  5.  "Formats, Definitions and Metrics" highlights qcML again.

When the PSI-SC removed the "Secretary" column from "Roles and Responsibilities" (https://www.psidev.info/roles) it was to move Wout Bittremieux's name to co-chair, replacing Stefan Tenzer's name.  I see that "Secretary" vanished, but that removed Wout's name entirely!

Mathias, the page lists you as our website maintainer.  Would you coordinate with Chuqiao Gong to update this information?

Thanks,
Dave

[Psidev-qc-dev] Schedule PSI Spring Meeting 2021

[Wout B. <wbi...@he...>]

Dear colleagues,

Please find below the latest schedule for the QC track during the PSI 
2021 Spring Meeting.

Notable changes are that we will have a joint session with the MS 
working group on Monday morning to discuss affinity-based workflows. 
These are new proteomics technologies (non-mass spec based) for which 
the idea is to build QC in on the ground floor, so they will certainly 
be able to benefit from our input.

I have also included some additional details for the other sessions 
where I think it would be useful to hear from specific people. Please 
consult the schedule below and maybe prepare a little bit if necessary. 
Feel free to reply to the mailing list, or even better on Slack during 
the meeting for faster communication.

I am looking forward to seeing you all this week!

Best,
Wout

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


*Schedule*


*Monday Session 1 - 8:00am PDT, 15:00 GMT, 16:00 CET*

*Topic:* 30 min Welcome and Introductions (Eric Deutsch)

*Zoom:* 
https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09 
<https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09> 
(password: hupopsi)

*Topic:* Affinity-based Workflows

*Zoom:* 
https://isbscience.zoom.us/j/92759368718?pwd=TlpJZ0NoRit6WFp0TjFCamtOM1RpZz09 
<https://isbscience.zoom.us/j/92759368718?pwd=TlpJZ0NoRit6WFp0TjFCamtOM1RpZz09>

5 min Welcome

15 min Ida Grundberg – Olink

15 min Sheri Wilcox – Somalogic

15 min Anita Bandrowski – The Antibody Registry

40 min Open Discussion


One hour break


*Monday Session 2 - 11:00a**m**PDT, 18:00 GMT, 19:00 CET*

*Topic:* Discussion of current and future mzQC implementations

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Welcome and Introductions (Dave Tabb)

- mzQC in Python: mzqc-pylib (Mathias Walzer)

- mzQC in R (Chris Bielow)

- mzQC in C# (Paul Brack)

- mzQC support in higher-level tools

- mzQC online validator

- Status of the libraries, future developments, and alternative 
programming languages.


---


*Tuesday Session 3 - 8:00am PDT, 15:00 GMT, 16:00 CET*

*Topic:* mzQC specification document

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Current status of the specification document and the review process 
(Mathias Walzer)

- Everyone: consult the specification document in advance! 
https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit 
<https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit>


One hour break


*Tuesday Session 4 - 11:00am PDT, 18:00 GMT, 19:00 CET*

*Topic:* mzQC specification document

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Status of the CV and future developments (Julian Uszkoreit)

- Example files in specification document appendix (Mathias Walzer, 
Chris Bielow, Wout Bittremieux)


---


*Wednesday Session 5 - 8:00am PDT, 15:00 GMT, 16:00 CET*

40 min *Plenary session*: The Complex Portal - Birgit Meldal

*Zoom: 
*https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09 
<https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09> 
(password: hupopsi)

*Topic:* mzQC / MIAPE-QC manuscript

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Outline of the manuscript (Wout Bittremieux)

- Collect use cases to demonstrate mzQC (everyone)


One hour break


*Wednesday Session 6 - 11:00am PDT, 18:00 GMT, 19:00 CET*

*Topic:* mzQC / MIAPE-QC manuscript

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Continued from the morning session

- Deeper discussion on MIAPE-QC (everyone)


---


*Thursday Session 7 - 8:00am PDT, 15:00 GMT, 16:00 CET*

*Topic:* PSI Semantic Metabolomics

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- Semantic Metabolomics (Steffen Neuman, Timo Sachsenberg)

- How to engage the metabolomics community? (Reza Salek)


One hour break


*Thursday Session 8 - 11:00am PDT, 18:00 GMT, 19:00 CET*

*Topic:* Identify future projects to which MS QC can contribute

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

- mzQC for top-down (Dave Tabb)

- Link with SDRF-Proteomics (Yasset?)


---


*Friday Session 9 - 8:00am PDT, 15:00 GMT, 16:00 CET*

60 min *Plenary Session*- Work Group summaries

60 min Cross WG sessions

*Zoom: 
*https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09 
<https://us02web.zoom.us/j/87431822456?pwd=VFRsOWxadk9UVUJ3dzF6OHgwckdQdz09> 
(password: hupopsi)


One hour break


*Friday Session 10 - 11:00am PDT, 18:00 GMT, 19:00 CET*

Topic: Flexible time for incomplete previous work

*Zoom:* https://embl-de.zoom.us/j/97793628177 
<https://embl-de.zoom.us/j/97793628177> (password: 667604)

[Psidev-qc-dev] Please register for our HUPO-PSI meeting

[David T. <dav...@pa...>]

Hi, folks.

Please go ahead to register for our late-March meeting (if you are coming).  You can find the link for this at the workshop website: http://www.psidev.info/hupo-psi-meeting-2021.

Thanks,
Dave