Member Info for Monkshood

Getting rather away from my expertise now... But where there are specific seriological markers then I don't see why not.
I am not sure of the basis of all of the antibiotic resistances. However there is no reason why you could not look for something like a B lactamase with an affirmer.

Interesting, thanks. There is a huge potential for 'lab on a chip' assays , again a good potential market for Avacta to be involved with.
The test may indicate that you have bacterial sepsis but not what the organism is, which is where the Maldi ToF comes in....

Re sepsis
https://pubmed.ncbi.nlm.nih.gov/30810264/
Looking in more detail at the pathways Adeptrix was originally targeting, their focus looked to be cancer research.

RD, I agree about the potential for synergy between the two companies. I have been looking at how to get exposure to Adeptrix as I think it also has a lot of potential.
Looking at their publications and early product offerings , it looks like Adeptrix was about targeting PTM's (post translational modifications ) in signalling pathways/networks . They then seemed to have realised that there is a broader utility and are expanding their platform as a potential form of ELISA replacement.
Mass specs are becoming increasingly important in medicine as you can multiplex analysis.
The instruments used for BAMS can also be used as a cost effective way for microbial identification in cases of sepsis.
If you want a really exciting application look at the Iknife research for cancer surgery.

I have been keeping an eye on this as well. Not topped up yet but will if it does ones of its sudden drops as it is inclined to do on occasions.
Results must be in a coulpe of weeks? Really interested to see how they have done, in particular their online sales. They were originally going to buy another company last year to achieve this but eventually developed it themselves, the lockdown should have helped them to establish a presence. I tried it and it was working well.
(and then of course there is the sanitiser...)

That is really where the clean up using the affirmer pull downs is important, to remove most of the background proteins/peptides. The m/z accuracy of the ToF's to 5 places also is pretty selective. If you have some nice toys then you can do ToF - MS/MS and check the peptide sequence.
My background was LC-MS/MS (on a triple Quad) using ' crude' cell lysates, but the LC simplified the complexity issue (and you have retention time as well) and the MS/ MS further reduces 'noise' even when working at unit m/z.

I would like to see what he is basing his numbers on. Aside form kit costs Maldi ToF's are a tad more expensive to purchase than a PRC machine... Are all those that are in hospitals sitting there unused?

Ophidian, short answer is, yes, it is possible.
Longer answer- Nucleotide changes for quantifying peptides/proteins are in some ways worse than for quantifying the same gene by PCR (provided it is not in the primer region)) . Although you can have silent changes(wobble on the third nucleotide), many will lead to a change in the MW of the peptide which is essentially what you are using as a 'filter' . Generally I would try and select for something that does not change where possible. If you know the likely changes (from published illumina sequencing) being you could look for these likely changes, if you are measuring multiple peptides (I usually use 3 if possible) then you could look for a change in the ratios of these.
You can also search through the data for 'atypical' m/z's, the issue (for good data) is back to standards, if you do not have one in the mix before the analysis on the MS then there is no accurate quantification.
Post translation modifications - eg glycosylation are also a potential problem as they to change the m/z
The rns was rather vague on method details - ‘unique method breaks up the spike protein’ - ‘identify fragments of the spike protein’ so I am still not clear as to their exact work flow.

Ophidian, that is a far more concise way of describing it.... Thanks
Cautious/ Ophidian, it nice to have some sensible scientific discussions about this.
Personally, having worked on MS based protein quant assays , I think that the time frame, so far, has been appropriate.

An alternative is, if it binds to the same sites as the ACE2 receptor then you could set up a competion assay with spike protein (to look at prevention of binding).

To expand this , if you look at the BAMS's store on the Adeptrix web page, then look at the number of 'upcoming products' you can see how easy it is to expand the range of target proteins they can offer. Each of these will require an antibody as part of the method. I assume that currently they use them under licence to whichever group/company provides them. Now factor in how easy it is to generate Affirmers to expand this platform and the other benefits of using them compared to antibodies (mono or polyclonal). It is very easy to visualise an array with a large number of target proteins as a routine hospital screening method, far better than carrying out lots of individual ELISA tests.
The potential long term income from this type of analysis even if only receiving a small amount per test would be substantial and not just a 'one disease wonder'.

Cautious , the nice thing with MS methods is that you can measure multiple peptides, so you could measure proeotypic markers both core and spike peptides at the same time. The only issue is, that for every peptide you measure you will need a control for the specific peptide measured, this will increase the assay development time and final cost of the kit.
When they announced the agreement with Adeptrix they said it was to increase testing capacity to complement PCR - (not replace it).
As I have said before , I do not see a huge value in this test per se, but I do in the collaboration because this type of test will become increasingly important in clinical screening for many conditions.

There is quite a bit to do to get these assays working. Assuming they do pulldowns then tryptic digests.
1) Selections of the proteotypic peptides - stability, reproducibility, linearity of response.
2)Sample prep - make affirmer conjugates , obtaining good saliva samples, optimise the pull downs, clean up washes - possible deglycosylation , tryptic digests.
3) Once they have an assay they will need isotopic control standards (several ways of achieving this) and then check out linearity sensitivity.
4) Check all this out on a range of samples - then scale up.
And everyone wants it done in a week....

But then they would need to get approval for multiple methods. I don't see this. I think that they will develop a single BAMS method which will run on a Maldi ToF , the individual vendors will optimise this for their instruments but that is not the same as running it on Triple/Orbi's

RK, not all Mass Specs are the same, the BAMS methods as per the Adeptrix web site are typicaly run on a maldi ToF. It will depend a bit on the method adopted but if they are using tryptic peptides then the platform(MS) is important. Different peptides are suited to different types of MS. If you are using a triple quad, then you would often select different peptides than if you were using a ToF or an Orbitrap. There have been no details of the controls but these would need to match the proteotypic tryptic peptide(s) selected (if this is what they do), so unless they generate a method that covers all options then it will be restricted to specific instruments (ToF's). Yes, most manufactures do make ToF's but my understanding is that they are not quite as ubiquitous in hospitals as implied. It is not a case of - a hospital has 'a MS' so they can run the assay.

Indeed, a very healthy markup for our 13p placing shares!
In the end I did not get all I wanted but was grateful that they at least allowed PI's to participate and also increased the amount available to us.
It is going to be interesting to watch how SCE grow over the next few years.

The test is to detect amylase as a marker for saliva - but the principles remain the same.

Sorry, had to go for tea and did not finish post - this is from a lateral flow test kit.

RSID™-Saliva Buffer components
The RSID™-Saliva laboratory kit includes extraction buffer (25 ml) and running buffer
(5 ml) that is required for use with the RSID™-Saliva kit. Each experiment included in
this validation document uses RSID™-Saliva extraction buffer for extraction of the
sample/s (extraction volumes are specified); the final volume of the sample to be tested
is brought to 100 µl with RSID™-Saliva running buffer. RSID™-Saliva extraction buffer
+ RSID™-Saliva running buffer (100 µl) is loaded onto the cassette and results are
recorded after 10 minutes.
RSID™-Saliva extraction buffer is designed to efficiently extract the protein a
amylase from questioned stains and swabs. RSID™-Saliva running buffer is designed
to dissolve the antibody-colloidal gold conjugate from the conjugate pad, maintain an
extract at the appropriate pH, and facilitate correct running of the test. Components of
the extraction and running buffer include buffer and salts (Tris, NaCl, KCl) for
physiological stability, a chelating agent (EDTA) for stability, detergents and surfactants
(Triton X-100 and Tween 20) for extraction efficiency and solubility maintenance,
protein (BSA) for reducing non-specific adsorption and loss, and a preservative (sodium
azide

'Patients were asked to pool saliva in their mouth for 1-2 minutes prior to collection, and gently spit 1-2 mL', this gave 85% positive compared to nasal swab.
I have seen a MS study that used a saline gargle. One report indicated that sampling from back of the throat (essentially gargling) was better

That should be 1000!