Quantifying the ∼75–95% of Peptides in DIA-MS Data Sets that Were Not Previously Quantified We have developed a novel algorithm termed GoldenHaystack (GH) that was designed for enhanced peptide quantification of data-independent acquisition liquid chromatography mass spectrometry (DIA-LC-MS) data files regardless of whether the amino acid sequences are subsequently assigned to the quantified peptide. The two central ideas behind GH are: (a) for sufficiently sized projects (e.g., ≥∼30 LC-MS files), pairs of peptides that coelute exactly in one subset of LC-MS files do not necessarily coelute exactly in a different subset of files, and (b) the ion intensity ratios between MS2 ions for any given peptide tend to stay the same across samples, but the ion intensity ratios of MS2 ions between different peptides tend to differ substantially across different samples. GH thus analyzes a project holistically: It uses multi-partite matching to match both MS2 (primarily) and MS1 (secondarily) ions across all samples, separates and regroups the MS ions into unique analyte quantifiable signatures (UAQS), reduces stochastic noise, and then quantifies those UAQS. In this paper, GH is compared to DIA-NN, a common algorithm used in DIA-MS proteomic analysis, and we demonstrate that GH (a) quantifies and identifies with better FDR accuracy known peptides found in FASTA search spaces (∼5–25% of analytes in DIA-MS data sets), (b) quantifies the remaining ∼75–95% of unassigned peptides that would be typically unquantified and unreported, and (c) runs ∼40–200× faster (or ∼1–10× faster than the LC-MS). Specifically, without a FASTA or spectral library, GH can deconvolute and accurately quantify chimeric LC-MS spectra. The use of a FASTA file occurs during an optional peptide identification step and is deployed only after the analytes in the MS files have already been quantified. We provide details of GH performance on several existing proteomics data sets, including plasma, cerebrospinal fluid, and cells.

Quantifying the ∼75–95% of Peptides in DIA-MS Data Sets that Were Not Previously Quantified | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Quantifying the ∼75–95% of Peptides in DIA-MS Data Sets that Were Not Previously Quantified We have developed a novel algorithm termed GoldenHaystack (GH) that was designed for enhanced peptide quantification of data-independent acquisition liquid chromatography mass spectrometry (DIA-LC-MS...

Quantifying the ∼75–95% of Peptides in DIA-MS Data Sets that Were Not Previously Quantified | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Excited to have our new mass spectrometry search engine for DIA which can easily handle orbitap astral data. Give it a try. Pmid: 41636803

#HUPO2025 many thanks to Jenny, Marie and Mathieu for hosting such an inspiring and beautifully organized meeting in Toronto! 👍👏The science, energy and community spirit were truly exceptional! Excited for the bright future of proteomics! 😀

At American Heart Association meeting in New Orleans-learning and dreaming up ways ti use proteomics to help cure heart disease.

Automation rules

See you there

We are delighted to inform you that BSPR 2026 will be held at the @ebi.embl.org campus in Cambridge from the 13th to the 15th of July. Make sure to save the data and join us for the a meeting full of great science focused on British & Irish Proteomics.

#proteomics #BSPR2026 #massspectrometry

It’s not a lack of interest but a technology limitation which, fortunately, continued to advance. PTMs, Structure, function are all part of proteomics.

Truly sadden to hear this.

An Itzy Bitzy Atlas™ of human proteins, feat. heart (part II).

The BBB www.economist.com/leaders/2025...

I will not watch or support this network

Shame on the Trump government-

Good question- meant broadly such as proteolyzed/modified forms of traditional proteins, synthesis from circular DNA or unexpected splicing and other species that maybe in our samples.

Native, Spatiotemporal Profiling of the Global Human Regulome The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...

Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social !

www.biorxiv.org/content/10.1...

This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.

1/?

this is really exciting and a reason to do mass spectrometry - find new proteins!!

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry
www.nature.com/articles/s41...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

We’re excited to announce the publication of Cascadia, our new de novo sequencing model designed for DIA data. By extending the transformer architecture to fully capture the complexities of DIA data, we achieve state-of-the-art performance.

www.nature.com/articles/s41...

CMA reflects on National Indigenous Peoples Day On this National Indigenous Peoples Day, the Canadian Medical Association (CMA) reflects on the rich history, strength and resilience of First Nations, Inuit and Métis Peoples.  This year marks the 10...

On this National Indigenous Peoples Day, we reflect on the rich history and resilience of First Nations, Inuit and Métis Peoples. We also recognize the importance of acknowledging the truth, moving forward with humility, and committing to culturally safe care for all #IndigenousPeoples.

Today RFK Jr took the single biggest step towards destroying childhood vaccines

When @nytimes asked me in December whether RFK could kill the vaccine program - I said he’d have to remove CDCs ACIP

And… that’s exactly what he just did today

Not good-just like that we cannot trust CDC on vaccines

@standupforscience.bsky.social. I just donated to fight for science and its impactfulness across all of life.

@standupforscience.bsky.social

Happy to transition from X, join the BlueSky community, and reconnect with ID and AMS colleagues across the globe. 🙂

PRIDE 2025: One Story. One Future. | GLAAD PRIDE 2025: One Story. One Future. stands as a call to action this Pride Month, urging the LGBTQ community and its allies to unite in defense of equality, love, and freedom.

Pride has always been powered by storytellers — the creators and truth-tellers who dare to envision a more just world. Our stories only reinforce that LGBTQ people are in every American family and share American values of fairness and the freedom to be who you are. (1/3)
glaad.org/pride-2025/

"South Florida weatherman tells viewers he can't accurately predict hurricanes because of government cuts"

Source:
old.reddit.com/r/PublicFrea...

We are excited to share that our Director of Proteomics Research, Dr. Sasha Singh, will be speaking at #FOGBoston at the end of this month! Registration is free for over 90% of attendees, so don't miss out! Reserve your spot at hubs.la/Q03cHRdb0. #genomics #biodata

Got to celebrate with friends at the SoCA group at ASMS- inventions drive knowledge.

Today, the ERC formally adopted a decision to increase its support for researchers moving to Europe.

On top of its normal grants, the ERC offers 'start-up' funding to help PIs establish laboratories / research teams in Europe.

This extra funding is now x2 (up to €2 million!)

europa.eu/!6Vdgmp

At the international society of heart research in beautiful Nara. Science is amazing.