Dear Members of the COVID-19 Mass Spectrometry Coalition,
Many thanks to all of you for signing up, it has been uplifting and at time overwhelming to connect with you all in these awful times.
We have managed to collect all of your details on our website – please do check that we got it right.
We have more than 220 scientists signed up from 18 countries – this is truly great, and our numbers are growing all the time.
We also have support from major manufacturers, and from the CAMS consortium and major pharmaceutical companies which is also great many thanks.
To further populate this effort, and to categorise the science that each member will perform, we encourage everyone to go to this web form
(Please note this is the same form used to sign up in our website. If you signed up recently there is no need to fill it in again and we do have a record of your expertise)
Once you have filled that in we can use it to create a directory of experts for the work that will be done over the coming months.
We have identified areas where mass spectrometry will make a difference: Omics (proteomics, metabolomics, glycomics and lipidomics); Protein dynamics and interactions; In situ analysis; Data processing curation and open data. We ask that you tell us which of these areas you are in.
We then propose to have working group leads in each area, and these can be international contact points to help streamline efforts and to share best practice. Please let us know if you wish to be a working group lead.
As we form this coalition we are aware that we must bring together national actions and work collectively where it will maximise benefit. To manage this we have a five point plan of action.
1. National Contacts
We recommend each country has national contacts for their COVID-19 MS actions, many thanks for the offers for this role from some already. For countries where we do not yet have a champion please contact us to let us know. We also recommend that countries have national contacts for sample collection protocols.
2. Patient sample collection, ethics and health and safety
We recognise that there are different processes in different countries for obtaining samples and the ethics around this may vary. We recommend that people adopt the WHO adopted ISARIC protocols where ever possible, https://isaric.tghn.org/. We would like to hear from people on how they have managed with the H&S for handle samples and suggest we can all help each other with evidence of what has worked.
3. Patient sample processing for mass spectrometry
We have amassed a number of protocols for each of the experimental procedures listed above, we will list these and where possible references to them on our website, to help with new studies. We recognise that most samples from hospital patients are likely to be blood/plasma/serum, but also we are keen to have protocols for other biofluids, for example urine, bronchial lavage and from throat/nose swabs
4. Data acquisition and processing
We have the offers of support from the manufacturers in these areas as well as from many expert labs. We expect that all of you will process the data you generate with your favourite programs/tools but again it would be good to share common practice. We have a lot of different platforms and methods, but there will be common features. Please get in touch if you can offer help here.
5. Open data repositories
Critical to our collective effort is how we manage the data. We suggest that for omics data you use a data repository (ideally PRIDE for proteomics datasets, as part of ProteomeXchange), and that you tell us the accession number. PRIDE enables the inclusion of the submitted datasets in the EMBL-EBI COVID-19 data portal (https://www.covid19dataportal.org/). After deposition we will record these along with the requisite metadata to identify the datasets. We will soon be updating the website with a dedicated page where you can submit this information. The website will also be updated regularly so that many researchers can access the processed data. It is through this that we will gain the most and most quickly. For native data on recombinant viral antigens get in touch as we will make the data repository and we will curate that data for all to examine and to compare to data from patient samples
We are applying for funds to help our national effort here in the UK and also to support the collaborative effort. We will be happy to share these applications with anyone who wishes to make similar funding applications.
Please get in touch, spread the word, and let’s work together to map this virus and its effects.
Perdi Barran, Frank Sobott, Kostas Thalassinos and all of the COVID-19 MS Coalition.
16 April 2020