iiinova — where your digital self keeps evolving

Chris Ashwood @cashwood.proteaglyco.com · 16/10/2026

Scary to see this as a table of contents graphic for one of the top ACS journals. I feel like even a quick glance by the authors would have noticed that T3 and T4 have identically incorrect structures.

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Chris Ashwood @cashwood.proteaglyco.com · 16/10/2026

A question came up in our Skyline course about if we could use an MCP (model context protocol) to have an LLM modify and prepare our document. Thanks to efforts by the Skyline team, it's possible. Here's an example, adding a random 20 glycan molecules to a Skyline document. No clicking needed.

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Chris Ashwood @cashwood.proteaglyco.com · 15/10/2026

While conferences are great, I really enjoy convening the Skyline small molecule course because a big group of us (~50) get to dive deep into analysing small molecule data in Skyline. We've been lucky enough to have some great lecturers/instructors this year, covering lipidomics to ion mobility.

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Chris Ashwood @cashwood.proteaglyco.com · 13/10/2026

Bad news for anyone not from a university that is trying to use ChatGPT or Claude for #glycotime research. Any time part of the content involves viruses, the request gets shut down. I moved from Claude because of this issue but it looks like an attempt to increase subscriptions for GPT "Rosalind"

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Chris Ashwood @cashwood.proteaglyco.com · 12/10/2026

Beyond the paper, the very same N-glycan calibration standards used in this publication will be commercially available through @proteaglyco.bsky.social within the week, enabling other laboratories to benchmark their own LC-MS workflows against a common reference.

A set of 6 vials containing a matrix matched calibration curve of glycans

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Chris Ashwood @cashwood.proteaglyco.com · 01/10/2026

We were hesitant about such an approach, due to the potential loss of glycome specificity resulting from the mixed glycomes, but surprisingly, we see higher glycan intensities AND the same structures are specifically attributed to the correct glycome.

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Chris Ashwood @cashwood.proteaglyco.com · 01/10/2026

It was great to attend #HUPO2026 and catch up with new friends and old. Here's our (@maiakelly.bsky.social) main poster for the conference, achieving the most comprehensive representation of the glycome to date with N-, O-, GSL-, and free- glycans acquired in a single LC-MS run. #glycotime

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Chris Ashwood @cashwood.proteaglyco.com · 27/09/2026

One thing I don’t see enough of, on social media, for these conferences is SWAG. Please find below what I’ve found so far at #HUPO2026

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Chris Ashwood @cashwood.proteaglyco.com · 14/09/2026

Recently, we evaluated DIA compared to DDA and our real-time glycomics method (basically, inclusion list-based DDA). DIA doesn't give us the sensitivity we need for structure. One benefit of DDA (or GlycoRTMS) is that it can accumulate for long time compared to the comprehensive but insensitive DIA

GlycoRTMS provides greater precursor-specific MS² spectral depth than DDA and DIA. A Comparison of MS² acquisition parameters; DIA used 68 m/z isolation windows across 570–1800 m/z to maintain cycle time. B Apex MS² spectra of the same biantennary disialylated N-glycan, showing increased spectral complexity with DIA. C Product-ion intensity distributions showing composition-confirming ions across methods, while lower-abundance structurally informative ions were detected only by GlycoRTMS.

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Chris Ashwood @cashwood.proteaglyco.com · 09/09/2026

That’s some pretty high res mass photometry! It’s a very clean distribution which makes the interpretation clear.

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Chris Ashwood @cashwood.proteaglyco.com · 31/08/2026

Thanks to valuable reviewer feedback, we've updated our GlyComboCLI software (and accompanying preprint) which includes: • GlyTouCan integration for glycan compositions • Strengthened software distribution and reproducibility • Expanded biological validation www.biorxiv.org/content/10.6...

New Figure 3 GlyComboCLI reproduces qualitative and quantitative features of a published human serum N-glycome. A Venn diagram comparing glycan compositions reported in the original study with GlyComboCLI assignments following isotopic-envelope filtering. B Rank trajectory plot comparing glycan abundance ranks derived from published glycan intensities, GlyComboCLI MS2 scan total ion current, and Skyline MS1 peak-area integration.

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Chris Ashwood @cashwood.proteaglyco.com · 10/08/2026

A nice memorial for Vern Reinhold, who passed away on Monday. He was a leading figure in carbohydrate analysis by MS, particularly multi-stage MSn. His papers were essential reading for us in our PhDs at Macquarie.

Dear Colleagues,

Dr. Vernon Reinhold passed away on Monday, August 3, 2026. Vern was a past president of the Society for Glycobiology (1999) and the 2015 recipient of the Rosalind Kornfeld Award for Lifetime Achievement in Glycobiology.
He had a remarkable life and career, ranging from service in the U.S. Navy Seabees to degrees from the University of New Hampshire and the University of Vermont, and post-doctoral work with Roger Jeanloz at Harvard Medical School and Klaus Biemann at MIT. (see his Kornfeld Award citation for details).

Vern would stay on at Harvard for 25 years developing cutting-edge mass spectrometry-based approaches for elucidating carbohydrate structures before returning to his roots at the University of New Hampshire where he completed his career as a Professor of Biochemistry and Chemistry, developing and directing the Glycomics Center.

Vern pioneered the use of ion-trap mass spectrometers for MSn of glycoconjugates to determine sequence, topology, linkage, and branching of glycans. His three back-to-back-to back manuscripts in Analytical Chemistry in 2005 are classics.

Anyone who knew Vern is aware of his vocal advocacy for rigorous approaches to glycan structure determination and his commitment to open discussion of technical challenges in the field, leading to his founding of the International Charles Warren Workshop on Glycoconjugate Analysis that meets biennially.

I was fortunate to learn both mass spectrometry and carbohydrate chemistry from Vern. He was an inspiring, rigorous, and compassionate mentor. In recent years Vern was still thoughtful about technical problems in carbohydrate sequencing, sometimes calling to share an idea.
His energy, commitment, and good humor will be sorely missed.

Doug Sheeley
National Institutes of Health

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Chris Ashwood @cashwood.proteaglyco.com · 16/07/2026

We compared LC–MS with DMB–LC–FLR because the latter is the established method for sialic acid quantitation. The LC-FLR background limited NeuGc detection to 2 orders of magnitude, while LC–MS reached ≥3 and retained the intact N-glycan context, clearly defining the limitation of the FLR approach.

Sample workflow for DMB-labelled sialic acid analysis for absolute quantitation of Neu5Ac and Neu5Gc is represented in Panel A. Linearity is achieve over ~3 orders of magnitude dyanmic range, starting at 1000 picograms of Neu5Gc, shown in Panel B. Panel C is the calibration curve from Figure 3 but representing the monosaccharide quantitation results, with no peak detected at the lowest two calibration values. Panel D has labelled chromatograms for the monosaccharide analysis, demonstrating barely increased signal over noise for the 1% Neu5Gc abundance tube, LLOQ.

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Chris Ashwood @cashwood.proteaglyco.com · 16/07/2026

Calibration curves turn “detected” into assay-specific quantitative claims. LLOQ varied by MS site and glycan. The widest dynamic range setup detected Neu5Gc-bearing N-glycans in neat human serum at ~0.01% of total sialylation. This also explains the varied reporting of NeuGc in human samples

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Chris Ashwood @cashwood.proteaglyco.com · 16/07/2026

At low intensity, a precursor m/z alone is not enough. We combined isotopic fit, PGC retention and MS2 to separate true Neu5Gc signal from noise, observing idotp decreasing with concentration. Search rules should reflect the fragmentation method: re-CID does not retain the diagnostic 306.08 ion

Panel A represents isotopic dot product values in a grid, reflecting the increasing dilution factor and the corresponding decrease idotp values. A chromatogram is represented in Panel B, demonstrating Neu5Gc- eluting before Neu5Ac- containing N-glycans. Panels C-F represent the different fragmentation spectra, with both resonant CID approaches generating the predominant charge-reduced precursor after loss of a single sialic acid, whereas beam-type CID spectra is more heterogenous in terms of product ion diversity.

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Chris Ashwood @cashwood.proteaglyco.com · 16/07/2026

To test low-abundance Neu5Gc in a realistic background, we serially diluted a Neu5Gc-rich N-glycome into human-serum N-glycans The six-sample set, leveraging matrix-matched calibration curves (shout out @lindsaykpino.com) spans 4 orders of magnitude and ensures results are quantitatively informative

Labelled mass spectra with panel A representing a Neu5Gc enriched N-glycome, and panel B representing a Neu5Ac enriched N-glycome, from human serum. The matrix matched calibration curve, made up of repeated 10x dilution of the Neu5Gc enriched N-glycome using Neu5Ac glycans from human serum, for a total of 6 tubes. Panel D visualises the expected sensitive results through a linear calibration curve while the potential less sensitive results are visualised with a linear curve that flattens out at the middle analyte concentration. Panel E represents the data analysis workflow, identifying glycan compositions with GlyCombo to generate a peak list which is used for quantitation, enabling calibration curves to be created for each glycan of interest.

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Chris Ashwood @cashwood.proteaglyco.com · 15/07/2026

In case people forget about the heavily "inspired" preprint by Nanomics in 2024, here's one comparison:

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Chris Ashwood @cashwood.proteaglyco.com · 14/07/2026

Big trouble in a nano world. It has been building up to this since the Nanomics preprint was disclosed that "heavily borrowed" elements from the Seer Astral marketing product notes. I'm not a lawyer, but Seer has the most compelling case thus far.

"On May 28, 2026, Seer, Inc. and The Brigham and Women's Hospital, Inc. (collectively “Seer”) filed a complaint with the U.S. International Trade Commission (“ITC”), alleging that Nanomics Biotechnology Co., Ltd. (“Nanomics”) infringes five different Seer patents. The complaint was filed without proper due diligence by Seer and is based in critical aspects on articles describing an experimental product that was never sold in the United States rather than Nanomics’ actual commercial products.

Nanomics categorically rejects Seer’s baseless allegations of patent infringement. Nanomics’ actual products imported to the U.S. are fundamentally different from Seer’s patents. As described by Seer itself in its ITC Complaint, what Seer purported to invent was “combining multiple, non-specific nanoparticles, each with different physicochemical properties, to capture and analyze the results from the resulting protein coronas.” In contrast, Nanomics uses a single particle approach which is completely distinct from Seer’s patents. Nanomics also does not infringe any valid claims of one of Seer’s patents describing a mass spectrometer coupled to a proteomics sample preparation device.

Nanomics has developed its own proprietary proteomics products which have been well-received in the U.S. market and have distinct advantages over Seer’s products. Nanomics views Seer’s allegations as nothing more than a misguided attempt by Seer to divert the attention of shareholders and the public from Seer’s severe value reduction— including an approximately 97% decline in shareholder return since its IPO and hundreds of millions of dollars in cumulative net losses reported in its SEC filings. It is regrettable that Seer has resorted to litigation instead of fair competition in the marketplace, rejecting a reasonable path to resolution and choosing to further burn shareholder money on a meritless case that does nothing to improve the company’s product competitiveness and only worsens its finan…

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Chris Ashwood @cashwood.proteaglyco.com · 06/07/2026

It's quite a clear increase in the oxonium ion-containing MS2 spectra, and the resulting increase in glycopeptide IDs.

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Chris Ashwood @cashwood.proteaglyco.com · 03/07/2026

Carbohydrates benefit from MS3 analysis, but it is slow and reduces our MS2 coverage, limiting uptake. Gating MS3 on both a glycan composition match and a diagnostic ion (m/z 332), it becomes chromatography-compatible. This pinned down product ions (m/z 152, 167) unique to O-acetylated Neu5Ac.

Figure 4 Real-time triggering of MS3 enables efficient, chromatography-compatible glycan structural analysis. A Overall workflow for real-time MS3 triggering with an O-acetylated Neu5Ac diagnostic ion. B A small subset of MS2 scans satisfy both correct precursor mass and diagnostic ion presence. C Precursor filtering to glycans is required to ensure MS3 triggering on O-acetylated glycans. D Real-time MS3 identifies unique diagnostic ions for O-acetylation.

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Chris Ashwood @cashwood.proteaglyco.com · 03/07/2026

Normalised collision energy (NCE) is calibrated on caffeine, a peptide, and Ultramark, not sugars. So we built charge-state-specific CE equations for glycans. Where fixed NCE gave near-identical, incomplete spectra, the calibrated approach produced full fragment ladders across sialic acid polymers.

Figure 3 Collision energy adjustment improves glycan coverage compared to fixed NCE. A Optimisation of Neu5Ac polymer optimal collision energy to develop CE correction factors for real-time MS. B Charge state-specific collision energy optimisation curves reveal standard normalised collision energy is unsuitable for multiply-charged oligosaccharides.

C Fixed NCE results in insufficient oligosaccharide fragment coverage. D Corrected NCE results in complete fragment series for oligosaccharides.

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Chris Ashwood @cashwood.proteaglyco.com · 03/07/2026

The usual DDA rules (intensity rank, skip +1 etc.) were built for proteomics and fail glycans, which span many charge states and vary wildly in intensity. By prioritising precursors that match glycans instead of raw intensity, GlycoRTMS sampled deeper, doubling MS2 coverage of a polysaccharide.

Figure 1 GlycoRTMS contextualises real-time decision-making with glycan-specific context. A The real-time assignment of glycan compositions from GlyCombo to MS1 precursors enables real-time MS2 and MS3 scans. B Outcomes achieved by real-time contextualisation of observed glycans, including precursor prioritisation, glycan-specific collision energy equations, and informed MS3 triggers

Figure 2 Real-time glycan assignment improves MS2 depth through prioritisation of precursors assigned to hyaluronic acid subunits. A Glycan prioritisation approach for acid hydrolysed hyaluronic acid. B Intensity rank distribution of glycans compared to background, across an LC-MS run. C-D Glycan prioritisation enables detection and characterisation of less intense, larger hyaluronic acid subunits

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Chris Ashwood @cashwood.proteaglyco.com · 02/07/2026

Claude says your reply was lazy because you used AI to critique my critique. Ironic. Don’t worry, I was allowed to use the most powerful Fable 5 model for this one.

Claude response to my prompt, that Hiren was being mean to me on Bluesky via Claude:

“I could pull up your original post about the Claude Science launch, but Bluesky’s reply threads don’t load for me, so I can’t actually see what Hiren Joshi posted. If you paste the reply here, I can react to the specifics.

A couple of thoughts in the meantime, though. On how to feel: getting dunked on stings, but someone outsourcing their snark to an AI is usually a sign they wanted a zinger more than a real argument. It says more about their effort level than about your point — and there’s some irony in someone using Claude to dismiss a critique of an Anthropic product.

On how to respond: your options are basically ignore it, respond to the substance only (“happy to discuss, but I’d rather hear your view than Claude’s”), or lean into the humor of the situation. What lands best depends on what the reply actually said and how much you care about the relationship — so paste it if you want a read on it.

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Chris Ashwood @cashwood.proteaglyco.com · 24/06/2026

"Raw data is available upon reasonable request to the corresponding author"

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Chris Ashwood @cashwood.proteaglyco.com · 19/06/2026

Sounds like the IAPI is coming to Astrals for the first time. Unsure on the details, if this is for the next Astral model or if it’s able to be used on existing installs. As posted by Karl Mechtler at Makarov’s 60th celebration.

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Chris Ashwood @cashwood.proteaglyco.com · 16/06/2026

Here’s the part everyone is curious about: UV curing of the polymer

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Chris Ashwood @cashwood.proteaglyco.com · 09/06/2026

The latest Skyline update has a great quality of life feature for ion mobility users. It's the new mobilogram window! With the heatmap, you can't quite make out the bimodal distribution, but with this mobilogram, it's crystal clear.

Skyline window showing the new mobilogram plot, highlighted in red.

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Chris Ashwood @cashwood.proteaglyco.com · 08/06/2026

I've spent the weekend catching up on #ASMS2026 talks, and this Q/A session was my highlight so far. Context: The interested audience member was trying to shout instead of using the mic (please don't, it's hard for online people to hear the question)

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Chris Ashwood @cashwood.proteaglyco.com · 05/06/2026

I mostly bring glycans to the mass spec, but today, I’m bringing myself to the glycans (marine)

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Chris Ashwood @cashwood.proteaglyco.com · 01/06/2026

Sciex has released a new version of the 5500 QQQ, called the Novus v55. Also incorporates the Optiflow ion source from the 7500+. Interesting move but makes sense given how many people I see sticking with their older Sciex instruments.

SCIEX
novus V55 system
The SCIEX novus V55 system is a new nominal mass triple quadrupole mass spectrometer positioned at the center of the SCIEX portfolio, purpose built to deliver high performance and operational efficiency for environmental and food testing laboratories. Leveraging more than 50 years of proven SCIEX reliability, the novus V55 extends this legacy with new innovations tailored to the demands of modern, high throughput testing environments. A key innovation of the novus V55 system is the accelerated MRM (aeMRM) technology, which enables acquisition speeds of up to 1000 MRM transitions per second. This ultrafast capability makes the system ideally suited for laboratories running large analyte panels, high plex screening methods, and multi class quantitative workflows, without compromising data quality, sensitivity, or precision. We will demonstrate the application of aeMRM technology for the analysis of approximately 500 pesticides in food, representing nearly 1400 MRM transitions. By leveraging faster dwell and pause times, the total method runtime was reduced from 30 minutes to 20 minutes, while maintaining sensitivity and sufficient data points across the chromatographic peaks. These results highlight the ability of the novus V55 system to significantly improve laboratory throughput while preserving analytical performance. In addition to fast acquisition, the novus V55 system incorporates the advanced OptiFlow ion source from the 7500+ system and the industry proven curtain gas technology, delivering exceptional robustness for routine analysis. This robustness was demonstrated through approximately 4200 consecutive pesticide injections across a diverse range of food matrices (salmon, kale, spice powder, avocado), corresponding to more than five weeks of continuous operation with consistent performance. The versatility of the novus V55 platform will also be demonstrated for PFAS analysis, including drinking water testing using EPA Method 533 and en…

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Chris Ashwood @cashwood.proteaglyco.com · 01/06/2026

ASMS2026 is looking like the year of the proteoform.

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Chris Ashwood @cashwood.proteaglyco.com · 29/05/2026

Stick one of these babies on your Apex and boom, easily 20-30% more IDs

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Chris Ashwood @cashwood.proteaglyco.com · 28/05/2026

Hooray, all the major MS vendors are funding Skyline now.

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Chris Ashwood @cashwood.proteaglyco.com · 28/05/2026

Brendan Maclean presenting the status of the Skyline project, after almost 18 years of development.

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Chris Ashwood @cashwood.proteaglyco.com · 28/05/2026

Next up is Evan Hubbard from Talus Bio, describing how the SCIEX ZenoTOF 8600 and Skyline work together to develop untargeted ZenoSWATH and ZT Scan methods.

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Chris Ashwood @cashwood.proteaglyco.com · 28/05/2026

An excellent presentation by @juank1892.bsky.social from Noortje de Haan's lab on how glycoproteomics with Skyline improves glycoproteomic data analysis. Works with any vendor's search output, delivering both MS1 and MS2 quality data, thanks to his unique approach to describe glycopeptide fragments

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Chris Ashwood @cashwood.proteaglyco.com · 28/05/2026

With both Matthias-based labs on this paper, you know it’s a big one. Just this panel alone is a significant amount of value

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Chris Ashwood @cashwood.proteaglyco.com · 26/05/2026

I find the sentiment that this is an AI "race" questionable, but I am proud to be Australian given where we place in this race.

A scatter plot, with the x axis as AI adoption from low to high, and the y axis labelled as AI sentiment from low to high.
Australia is one of the lowest in terms of AI sentiment, similar to Finland, however Finland has moderate AI adoption.
India and China have the highest AI sentiment and adoption rates.

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Chris Ashwood @cashwood.proteaglyco.com · 24/05/2026

Links: - Apex: www.thermofisher.com/order/catalo... - Excedion (not Pro): www.thermofisher.com/order/catalo...

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Chris Ashwood @cashwood.proteaglyco.com · 24/05/2026

Okay, here are the Thermo #ASMS2026 leak confirmations: - Tribrid Apex (the next Ascend + IRMPD) - Orbitrap Excedion is the downgraded version (240k max res) of the Orbitrap Excedion Pro. The name is going to cause a lot of confusion. Thanks go to my wonderful sources.

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Chris Ashwood @cashwood.proteaglyco.com · 22/05/2026

It's a bit nerdy but academic family trees fascinate me. You get to see the scientific ideas that were had across the generations and how they changed. The tree was missing a link (Athelstan Beckwith) but with that elucidated (thanks to a 1967 thesis), it has all come together.

An academic family tree for Nicki Packer

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Chris Ashwood @cashwood.proteaglyco.com · 20/05/2026

Psssssst. I think there has been a leak about Evosep's #ASMS2026 announcement.

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Chris Ashwood @cashwood.proteaglyco.com · 19/05/2026

Two grants for MS and #glycotime! 1. Sifting through the air by mass spectrometry. SYFT and QUT. 2. Engineering immobilised glycan platforms. Culturon and UNSW.

Professor Megan Lord; Professor Marcela Bilek; Dr Stuart Fraser; Dr Jonathan Yeow Engineering immobilised glycan platforms. This project will develop next-generation screening platforms for human-use products by leveraging plasma technology to stably immobilise glycans on substrates, authentically replicating the cell surface glycocalyx. This will enable a reproducible, high-throughput, and cost-effective method for testing interactions with human cells. By moving beyond animal models and cell lines, the platforms overcome key scientific and ethical limitations and advance understanding of glycocalyx-mediated biological responses. The project promotes skills transfer, researcher training and will strengthen Australia’s leadership in biomanufacturing and sustainable economic growth. The University of New South Wales CULTURON PTY LTD

Professor Stephen Blanksby; Associate Professor Branka Miljevic; Dr James Behrendorff; Dr Nicholas Demarais Sifting through the air by mass spectrometry. Real-time detection of trace volatiles in air is critical for the rapid assessment of: air-quality to protect human safety; the changing composition of Earth’s atmosphere and its effects on climate and; identifying the volatile emissions from biochemical processes. Industry partner Syft Technologies was the first to commercialise selected-ion flow tube mass spectrometers that are uniquely capable of meeting these critical needs. Here, Syft will partner with QUT to advance the sensitivity and selectivity of its instrumentation and thus advance understanding of Australia’s unique marine environments and drive innovation in precision fermentation. Queensland University of Technology SYFT TECHNOLOGIES

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Chris Ashwood @cashwood.proteaglyco.com · 19/05/2026

It’s a shame they couldn’t draw the oligomannose structures correctly, it undermines what looks to be a good study.

Galactose and mannose fucosylation on an oligomannose structure

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Chris Ashwood @cashwood.proteaglyco.com · 18/05/2026

I'm not so sure about the providing value aspect (and therefore the ROI). There are environmental, legal and ethical issues that make it net neutral at best. Here are 2024 survey results from ACS, more than 50% disagree that genAI substantially improves productivity: www.acs.org/content/dam/...

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Chris Ashwood @cashwood.proteaglyco.com · 18/05/2026

Single-Molecule Glycan Discrimination Using a Graphite Nanopore Chandan Kumar Das and Maria Fyta pubs.rsc.org/en/Content/A... It's a #glycotime version of nanopore seq, using carbon like our LC-MS. There is some capacity for discrimination, so maybe there will be a company exploiting this soon?

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