Jeffrey C.-F. Huang

TECHNICAL INNOVATION: We also demonstrated that I2MS for fragment ion analysis (I2MS2) increases catenin top-down sequence coverages from <1% to ~30%. We expect future instrumentation advances will improve proteoform-level analysis of these LARGE structural proteins/complexes. (7/7)

BIOLOGY TAKEAWAY: We proposed a catenin phospho-code—where combinatorial phosphorylation of these large proteoforms works with mechanical signals to drive cadherin–catenin organization and #adherensjunction function. (6/7)

Using bottom-up proteomics/antibodies, we confirmed that some phosphorylations appear constitutive, while others are more sensitive to myosin inhibition, raising the possibility of a mechano-sensitive “phospho-code” for cell-cell adhesion. (5/7)

Remarkably, catenin phosphorylation is sensitive to drugs that modulate #actomyosin contractility. We observed HYPER-phosphorylation on catenins under conditions that promote cell rounding and HYPO-phosphorylation when myosin activity was reduced. (4/7)

With Team @carajgottardi.bsky.social ‘s expertise in cell-cell adhesion, we purified cadherin-associated catenins and profiled their proteoforms using I2MS and found #phosphorylation to be the MAJOR modification. (3/7)

Team @nlkproteomics.bsky.social has developed individual ion mass spectrometry (I2MS) for proteoform analysis. We extend the current ~70 kDa mass limit beyond 100 kDa in this work. (2/7)

Intact Mass Profiling Reveals Phospho‐Proteoforms of the Catenins (85–110 kDa) Regulated by Actomyosin Contractility This study advances top-down individual ion mass spectrometry (I2MS) to profile intact phospho-proteoforms of β- and α-catenins (85–110 kDa) within cadherin–catenin complexes. By modulating actomyosi....

THRILLED to share our new publication in @angewandtechemie.bsky.social from #CLP & @nucdb.bsky.social "Intact Mass Profiling Reveals Phospho-Proteoforms of the Catenins (85–110 kDa) Regulated by Actomyosin Contractility” using TDMS to study LARGE catenin proteoforms. (1/7)
doi.org/10.1002/anie...

Heading to #HUPO2025! I’ll talk about our catenin phospho-code story and how top-down MS reveals how adhesion proteins respond to actomyosin force!

Thanks for the invite, #AFFINISEP!

Full story on bioRxiv 👉https://doi.org/10.1101/2025.09.06.674621

Neil Kelleher: The Human Proteoform Project Could Transform Medicine theanalyticalscienti...

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#proteomics #prot-article

🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7

High-performance proteomics at any chromatographic flow rate

These data follow the expected trends as though taken from a textbook !

They illustrate clearly the trade-offs between high and low flow rates.

Sigh…

The phosphorylated form of α-catenin localizes to the apical portion of adherens junctions. The image shows 3D surface rendering using Imaris software of a confocal image of a dividing kidney epithelial cell line (Madin–Darby canine kidney or MDCK cells). Phosphorylated α-catenin is shown in magenta and adherens junctions are in green.

🧪Phuong Le, Jeanne Quinn, @jfhorner.bsky.social @carajgottardi.bsky.social & co show that the adhesion protein α-catenin has a key modification that allows dividing cells to stay better connected to their neighbours, helping the tissue stick together during mechanical stress. doi.org/10.1242/bio....

The mass spectrometry research community at Chicago is thriving! Many thanks to the Chicago Mass Spec Interest Group for the invitation to share my catenin proteoform story in the inaugural event. It was a pleasure to meet with researchers at the beautiful CZbiohub space!

Looking forward to sharing my work at the Chicago Mass Spec Interest Group’s inaugural meeting!

It was a very fruitful #USHUPO2025 ! I was beyond thrilled to share our advances in catenin proteoform profiling and functional studies that will reveal the phospho-code in cell-cell adhesions. Many thanks to the conference organizers and participants!

Next steps for targeted protein degradation Modalities and applications of targeted protein degradation (TPD) have rapidly expanded the therapeutic possibilities of proximity induced pharmacology. Here, Krone et al. spotlight three focal points...

Next steps for targeted protein degradation: Cell Chemical Biology www.cell.com/cell-chemica... #TPD #PROTACs

Looking forward to attending the #USHUPO conference in Philly this weekend and sharing some early results in catenin proteoform profiling and our vision to build a story behind acto-myosin contractility regulation in cell-cell adhesion. Please join my talk next Wednesday and say hi!

Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications; thus, there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTM’s site localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system.

New manuscript from the lab to establish a Top Down MS platform using electron activated dissociation on the Sciex ZenoTOF 7600 is out at the Journal of Proteome Research!

pubs.acs.org/doi/full/10....

Standardized workflow for multiplexed charge detection mass spectrometry on orbitrap analyzers - Nature Protocols Orbitrap-based individual ion mass spectrometry enables charge detection mass spectrometry application on a broadly accessible mass spectrometry platform, enabling the analysis of complex mixtures tha...

Standardized workflow for multiplexed charge detection mass spectrometry on orbitrap analyzers #NatProtoc www.nature.com/articles/s41...

It was a tremendous pleasure to visit my alma mater National Taiwan University and give a talk on top-down proteomics and proteoform biology at the Institute of Biomedical Sciences earlier this week.

Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification analyticalsciencejou...

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#proteomics #prot-paper

Emerging opportunities for intact and native protein analysis using chemical proteomics www.sciencedirect.co...

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#proteomics #prot-paper

I love it when a place plays the Nutcracker during the holiday season, not All I Want For Christmas Is You on repeat 😝

Multi-Reflecting TOF MS for Analyzing Proteins This paper presents detailed results of previously reported protein studies conducted using a prototype multi-reflecting time-of-flight mass spectrome…

Multi-Reflecting TOF MS for Analyzing Proteins #IJMS www.sciencedirect.com/science/arti...

Intact Mass Proteomics Using a Proteoform Atlas Top-down proteomics, the characterization of intact proteoforms by tandem mass spectrometry, is the principal method for proteoform characterization in complex samples. Top-down proteomics relies on p...

Intact Mass Proteomics Using a Proteoform Atlas #JProteomeRes pubs.acs.org/doi/10.1021/...

This is another step towards assigning proteoform-specific functions!

Top-Down Stability of Proteins from Rates of Oxidation (TD-SPROX) Approach for Measuring Proteoform-Specific Folding Stability The crucial roles of proteoforms in biological processes and disease mechanisms have been increasingly recognized. However, the rate at which new proteoforms are being discovered using top-down proteomics has far outpaced the rate at which the functional significance of different proteoforms can be determined. Because of the close connection between protein folding and protein function, protein folding stability measurements on proteoforms have the potential to identify functionally significant proteoforms of a given protein. While a number of mass spectrometry-based proteomics methods for making protein folding stability measurements on the proteomic scale have been reported over the past decade, none have been interfaced with top-down proteomics. Described here is a top-down (TD) stability of proteins from the rates of oxidation (SPROX) approach for making proteoform specific folding stability measurements. This approach is validated using a mixture of three model proteins with well-characterized protein folding behavior by conventional SPROX as well as other more conventional biophysical techniques. The method is also used to evaluate the relative folding stabilities of the <30 kDa protein fraction isolated from an MCF-7 cell lysate. The relative folding stabilities of 150 proteoforms from 83 proteins were successfully characterized in the cell lysate analysis using the TD-SPROX approach.

Very happy to share my third major work this year (and first on 🦋)! This is a co-first work with the Fitzgerald group at Duke where they perform the SPROX protein folding stability assay and I figure out how to decribe the results using top-down proteomics!

doi.org/10.1021/acs....

Is “proteomics approach” the same thing as “proteomic approach”? I was under the impression that you should always add the s at the end of -omics, even as an adjective because it’s part of the word to show that we’re measuring thousands of targets at once. But I see people using proteomic without s.

Going home from the lab be like 🥶. First snow is Chicago!