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Latest Bruker or Thermo #TeamMassSpec instrument for #proteomics? Please share your honest experience (anonymously if you want)! Sometimes it is more than just the specs (ie. price, robustness, maintenance, software)

#massspectrometry

I thought it was quite mind boggling to see that around 10% of the protein in a standard yeast based bread is actually yeast protein! Here our #metaproteomics analysis of microbial protein in fermented foods
pubs.rsc.org/en/Content/A...
Congratulations to first authors Laura Winkler and Ayesha Awan

New OpenFold3 preview out! (OF3p2)

It closes the gap to AlphaFold3 for most modalities.

Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

🇫🇮🔬 We're at #FinnProt2026 in Espoo, Finland!

Our CTO Cristina Hernandez Rollan is presenting a poster with the latest from our R&D pipeline

👀 Stop by to get an early look at what's next from KPL!

#Proteomics #MassSpectrometry #TeamMassSpec

I initially thought the prices were in Danish kroner. Yikes!

#2 on my list of fave animals in the ocean, Bathyphysa. This is a siphonophore & it caught a fish! I wish I could touch it (don't touch it). @schmidtocean.bsky.social dive 743 part 2 #chilemargin #MarineLife

Seamless workflow of hydroxy acid-modified metal oxide chromatography for rapid and sensitive phosphoproteomics sample preparation Phosphoproteomics by liquid chromatography/tandem mass spectrometry requires efficient phosphopeptide enrichment, but conventional workflows are often time-consuming and prone to sample loss, particularly at low input. Here, we present Rapid Hydroxy Acid-Modified Metal Oxide Chromatography (Rapid HAMMOC), a streamlined, TiO2-based enrichment workflow that features three key improvements. First, we optimized the TiO2 column loading conditions and found that alternative pH-buffering agents and organic solvents, such as sodium bicarbonate combined with ethyl acetate, outperformed the commonly used Tris-based buffer with isopropanol. Second, to minimize sample loss and manual handling in desalting, phosphopeptides eluted under basic conditions were directly loaded onto a dual-membrane StageTip composed of stacked strong anion exchange (SAX) and reversed-phase styrene-divinylbenzene (SDB) membranes (SAX-SDB StageTip). Third, the addition of lauryl maltose neopentyl glycol (LMNG), which is readily removed during desalting, suppressed nonspecific adsorption. Rapid HAMMOC provided markedly improved sensitivity, identifying approximately 5,000 class I phosphosites from 5g of K562 cell digests, with a median 7.9-fold increase in intensity compared to the original workflow. Rapid HAMMOC also identified, on average, approximately 8,000 class I phosphosites from as little as 0.5 g input from HeLa, A549, and HCT116 cells. Furthermore, coupling Rapid HAMMOC with anti-puromycin immunoprecipitation enabled single-day profiling of nascent polypeptides from ultra-low input samples, yielding 2,310 high-confidence co-translational phosphosites. Beyond providing a practical enrichment workflow, this study offers broadly applicable insights that can be extended to other TiO2-based phosphoproteomic methods.

(BioRxiv All) Seamless workflow of hydroxy acid-modified metal oxide chromatography for rapid and sensitive phosphoproteomics sample preparation: Phosphoproteomics by liquid chromatography/tandem mass spectrometry requires efficient phosphopeptide enrichment, but conventional… #BioRxiv #MassSpecRSS

Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins, playing a pivotal role in various pathological processes. Mass spectrometry-based large-scale glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation in both physiological and pathological contexts. Traditionally, DDA glycopeptide assignment relies on information-dense MS2 spectra, containing sufficient fragmentation information to identify both the peptide and glycan moieties. Achieving this fragmentation can be difficult, especially for low-abundant glycopeptides and/or large, complex glycans. These glycopeptides are often not assigned using current data analysis software, yet they can be of biological relevance. Here, we introduce a method called match-between-glycans (MBG), which expands glycopeptide identification while maintaining the existing glycoproteome analysis workflow. MBG enables expanding the set of identified glycopeptides to include those without MS2 spectra, or with lower quality MS2 spectra, by looking for MS1 signals displaced from other identified glycopeptides by one or multiple monosaccharide unit(s). MBG can also identify glycans not included in the glycan database, such as those containing adducts or modifications, allowing these glycans to be recovered without a drastic expansion of the search space. Combined with target-decoy FDR control, we show this method is capable of accurately expanding glycopeptide identifications and providing a more complete quantitative profile of glycosylation at each glycosite. MBG is fully integrated into the glycoproteomics workflows in FragPipe, allowing seamless, one-click operation.

(BioRxiv All) Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe: Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins, playing a pivotal role in various pathological processes. Mass… #BioRxiv #MassSpecRSS

Maybe this is as controversial as not doing BCA before LC-MS proteomics:
“match-between-glycans (MBG), which expands glycopeptide identification…MBG enables expanding the set of identified glycopeptides to include those without MS2 spectra, or with lower quality MS2 spectra,”

You dun goofed!

Our latest #proteomics product to top off our Lys-C and Trypsin offerings. A high quality optimal premix of Lys-C and Trypsin that enables reproducible proteomic analysis! Make sure to follow @kplaps.bsky.social for more exciting news and updates!

#TeamMassSpec

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows - PubMed A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor information have been developed to overcome the reprod …

Check out the first author!
pubmed.ncbi.nlm.nih.gov/30671891/

Ehh yooo wtf!!

Looks like proteomics has hit the big time!

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

www.science.org/doi/10.1126/...

By 2028, all 4-character PDB IDs will be exhausted.

After that, all new entries will receive extended IDs: 12 characters total, formatted as pdb_ + 8 alphanumeric characters (pdb_1000axyz)

Test it from PDB Beta Archive

Read more: www.wwpdb.org/news/news?ye...

The Dolphin Head nebula in Canis Major constellation, photographed from my terrace

1/ The Dolphin Head (Sh2-308) is an emission nebula in the Canis Major region: a huge bubble created by material expelled by the star WR6, swept by its powerful stellar wind.
It’s also a target that drove me crazy for four years before I finally started to get a grip on it. ➡️

🔭
#Astrophotography

Closer

close enough?! (home made needle columns)

Me every single time i need to prepare a LCMS setup to run a couple of samples ...
#proteomics

Aside from the whisper network, how are #teammassspec finding out how much certain instrument models are down for (service delays, backordered parts, things breaking all the time, etc)?

From Croatia to MAHA: How an unapproved drug became the next hot peptide BPC-157 hasn't been approved by the FDA. But that hasn't stopped this buzzy drug from gaining traction – and attention from MAHA.

BPC-157 hasn't been approved by the FDA. But that hasn't stopped this buzzy drug from gaining traction – and attention from MAHA. www.statnews.com/2026/02/03/b...

Our recombinant, animal free, sustainable, artisanal 😁 Trypsin is here! High quality, high performance, drop in replacement for any existing #proteomics workflows.

Designed and produced in 🇩🇰🇪🇺

Zotero 8 is out, and we are very lucky to have such great open source software

Pervanadate-induced oxidation relieves autoinhibition of the protein tyrosine kinase SRC A widely used tyrosine phosphatase inhibitor also oxidizes and activates the tyrosine kinase SRC.

Pervanadate is more than just a phosphatase inhibitor!

Read our paper just published in #sciencesignaling showing that pervanadate oxidises and activates SRC kinase too.

Link: tinyurl.com/5ype7e2s

Thanks for the 'focus' by: @nshahlab.bsky.social tinyurl.com/54fcjds3

@babrahaminst.bsky.social

Single-cell proteomics is moving past descriptive snapshots to quantitative models of cellular regulation and biological mechanisms.

Come to #Boston this July to shape the next chapter and have your voice heard.

Abstract deadline: Apr 1, 2026.

single-cell.net/proteomics/s...

Trypsin is the workhorse of bottom-up #proteomics. But when was it first discovered? Lets try an emoji poll !

😇 1836
🤭 1876
😜 1897
🤑 1931

Reply with your guess!

Correct answer in the replies!

#TeamMassSpec

New publication alert! 📢

We collaborated with @jesperolsenlab.bsky.social to comprehensively characterize LysC homologs and study their impact on proteomic experiments.

For challenging samples, adding LysC can definitely make a difference in the data quality.

Congrats to all authors!

#proteomics

AutoPELSA: an automated sample preparation system for proteome-wide identification of target proteins of diverse ligands www.biorxiv.org/content/10.64898/2026.01...

To everyone who's supported us, bought from us, or just followed along to see what happens ... Thank you for a great year, you're the real MVPs!

2026 pipeline is looking spicy 🌶️ new products, big announcements I believe will push the field of #proteomics forward. Stay tuned.