iiinova — where your digital self keeps evolving

Thanks Bini. That is very useful to know. I think that quantitative proteomics has a way to go but it’s getting there. Need to add internal standards to general workflows though.

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That's what I was guessing. In the CRO I was working for before I retired 14 points across the peak was the minimum required which is rarely seen in proteomic experiments. Will be interesting to see how quantitative proteomics evolves and matures.

Astral and TIMS-TOF Ultra users I would be interested in how many points across the peak you are getting from your DIA experiments. If you can share gradient length and points across the peak as I would like to compare with the small mol CRO methods. Quantitative proteomics needs some rigour I think

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Just spent a week moving into a new house and totally exhausted. New house not so new though as built in 1576 so I now live in a Elizabethan farm house with very high oak beams. Just back at my desk organising some training and consulting so retirement is busy!!

Nick Morrice @pommie331.bsky.social · 25/02/2025

John doing his best Winston Churchill impersonation .

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Nick Morrice @pommie331.bsky.social · 22/02/2025

I would hope the Scottish government will do something to put the Orange one in his place. Ban him from visiting his golf courses in Scotland . That’s how you treat a petulant child.

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Nick Morrice @pommie331.bsky.social · 17/02/2025

First official day of retirement. I can highly recommend it. Just waiting for the trout season to open next month.

Nick Morrice @pommie331.bsky.social · 09/02/2025

Enjoy Albert. Fantastic part of the world and a trip to Wye River is worth it for the koalas and king parrots.

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Nick Morrice @pommie331.bsky.social · 29/01/2025

Nice thing about being retired is I can come to scotland to see the kids when I want. Also caught up with old colleagues at CRUK Scotland and MRCPPU in Dundee. Now off to Aberdeen.

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Nick Morrice @pommie331.bsky.social · 23/01/2025

Business as usual Matt. The orange one huffs and puffs but has to get both houses to approve any of his directives.

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Nick Morrice @pommie331.bsky.social · 21/01/2025

0.3mm i.d columns at 5-10ul/min were bulletproof unless it was a failed digest. Usually 2000-5000 injections before needing to be changed.

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Nick Morrice @pommie331.bsky.social · 21/01/2025

I have said this for years Luke. Micro is the way ahead and has been for me since 2011.

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Nick Morrice @pommie331.bsky.social · 19/01/2025

Lots of respect from me. Too many students and post docs use pre cast without ever knowing the ins and outs of SDS PAGE. Costs plenty too!!

Nick Morrice @pommie331.bsky.social · 19/01/2025

Self poured or pre-cast gels? I remember those days back in the 80's.

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Nick Morrice @pommie331.bsky.social · 18/01/2025

In CRO world a minimum of 14 points across the peak is required for accurate quantification. This means your MS has to be fast.

Nick Morrice @pommie331.bsky.social · 18/01/2025

I think we should mix and match. High in Fahrenheit and low in Celsius just to confuse people even more😉

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Nick Morrice @pommie331.bsky.social · 17/01/2025

I should really post science discussion here, but this was my son playing #2 Freed Hardmann in the NAIA last night

Nick Morrice @pommie331.bsky.social · 15/01/2025

Thanks Mike. Looking forward to more fishing mixed in with some science.

Nick Morrice @pommie331.bsky.social · 15/01/2025

Less than one month until I retire from full time work. I am going to offer training and consultancy from early march 2025, so if you know of anyone who would like training on LCMS systems or consultancy on proteomics sample prep etc please mention my name.

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Nick Morrice @pommie331.bsky.social · 15/01/2025

It is a cool comparison and yes I think Olink is only human proteins. As pointed out there is a conflict of interests from the authors but I think the study is sound and should be discussed. That’s what this place is for.

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Nick Morrice @pommie331.bsky.social · 14/01/2025

Nice review of plasma proteomics methods by Josh Coon and his group . However the perchloric acid treatment of plasma will lead to the formation of cysteic acid and methionine sulphone which is not mentioned for the DIA search. .https://www.biorxiv.org/content/10.1101/2025.01.08.632035v1

biorxiv.org

A Technical Evaluation of Plasma Proteomics Technologies

Plasma proteomic technologies are rapidly evolving and of critical importance to the field of biomedical research. Here we report a technical evaluation of six notable plasma proteomic technologies - ...

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Nick Morrice @pommie331.bsky.social · 13/01/2025

Standard 2.1mm columns from various vendors are around 700 pounds so price seems about right. If you want a validated column you need to pay I am afraid.

Nick Morrice @pommie331.bsky.social · 08/01/2025

I am doing HILIC of oligonucleotides ( I know!!) and the sodiation I am seeing must be coming from the LC even though it has been thoroughly washed. The ASO made up in ammonium acetate/acetonitrile/milliQ water shows no sign of sodiation when infused. Any ideas on how to reduce the sodiation?

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Nick Morrice @pommie331.bsky.social · 27/12/2024

I’m at the end of my career so I can be a grumpy old bugger. Things like this need to be rectified as zi currently work in a GRP company and this is not tolerated at all.

Nick Morrice @pommie331.bsky.social · 27/12/2024

Wouldn't it be refreashing to actually have a method in a paper that describes all the details. I love the reference to a previous paper that tells you absolutely nothing. So common and tolerated in our community.

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Nick Morrice @pommie331.bsky.social · 12/12/2024

Bang on Alexey. Some systems are randon number generators with relaxed filters applied to the data.

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Nick Morrice @pommie331.bsky.social · 10/12/2024

S/N filters in software would be a good start as they can filter out a lot of bad spectra. You will lose total i.d's ( not a bad thing) but have confidence that the i.d is based on a solid MSMS spectrum.

Nick Morrice @pommie331.bsky.social · 10/12/2024

Hard to beat a bit of manual curation Mike. It's slow, but I wouldn't share a phosphopeptide MSMS spectrum with colleagues unless I was absolutely sure. They would go off and make phospho antibodies and site directed mutagenesis, so if I was wrong I would waste a lot of grant money.

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Nick Morrice @pommie331.bsky.social · 09/12/2024

Anyone else feeling cleansed after de-X-ing themselves. I certainly do. Keep up the good converastions here where the sky is blue.

Nick Morrice @pommie331.bsky.social · 09/12/2024

Great to see Peter. I gave a seminar there in 1998 and at the end of the seminar Peter lit up a cigarette. I asked if this was the smoking room and he said where ever he is is the smoking room. I joined him as I still smoked in those days!!

Nick Morrice @pommie331.bsky.social · 06/12/2024

Plasma albumin measured using swath when observed using the swath microApp in Peakview is an excellent QC. You see the full MSMS spectrum , not just the XIC's. Only thing missing from this plugin was the TOFMS scan so you could compare MS1 and MS2 quant.

Nick Morrice @pommie331.bsky.social · 04/12/2024

A motley looking crew. Good to see so many familiar faces and Ole invited me to speak their way back in 1997.

Nick Morrice @pommie331.bsky.social · 03/12/2024

That quote was from ASMS in 2004 in Nashville. So true.

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Nick Morrice @pommie331.bsky.social · 03/12/2024

A true legend in the field. Wee done Peter.

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Nick Morrice @pommie331.bsky.social · 03/12/2024

I miss attending this meeting. Always top draw talks and networking.

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Nick Morrice @pommie331.bsky.social · 01/12/2024

I feel refreshed ; X account deleted.

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Nick Morrice @pommie331.bsky.social · 29/11/2024

Just like phosphorylation,O-glycans on Thr are more stable than on Ser, so always a chance of seeing the modified mass in a CID spectrum. EAD has the benefit of being very quick with reaction times of 10-25ms, so totally compatible with fast gradients.

Nick Morrice @pommie331.bsky.social · 29/11/2024

O-glycans, especially O-GlcNac don't b-eliminate water like pSer/pThr. You end up with a naked not dehydrated ser/thr. This is where EAD/EThCD does the business in preserving the O-Glycan.

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Nick Morrice @pommie331.bsky.social · 28/11/2024

Chicken over here is filled with water. One small bird produces nearly a pint of liquid to make gravy. Only way to make sure you have chicken and nothing but chicken is to slaughter your own.

Nick Morrice @pommie331.bsky.social · 26/11/2024

For many years I ran Edman sequencers and have seen the original Edman Begg sequencer in Melbourne. Loved reading off sequences and one in particular made me laugh. It was in a PEST domain and the sequence was EATME !!!