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@vaneykj.bsky.social

Proteomics, precision health, mass spectrometry, biomarkers, quantitative, changing medicine

42 Posts114 Follower109 Folgt
@vaneykj.bsky.social · 6mo ago

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) 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.

pubs.acs.org

@vaneykj.bsky.social · 6mo ago

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

Ying Ge@yingge2121.bsky.social · 9mo ago

#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! 😀

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@vaneykj.bsky.social · 9mo ago

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

Lindsay K Pino@lindsaykpino.com · last yr.

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/?

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...

biorxiv.org

Michael MacCoss @maccoss.bsky.social · last yr.

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...

nature.com

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wnoble.bsky.social@wnoble.bsky.social · last yr.

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...

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...

nature.com

Canadian Medical Association@cmadocs.bsky.social · last yr.

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.

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...

cma.ca

Michael Mina MD,PhD@michaelmina.bsky.social · last yr.

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

Sarah Kate Ellis@sarahkateellis.bsky.social · last yr.

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/

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.

glaad.org

Marc Veldhoen@marcveld.bsky.social · last yr.

Refusing to be complicit in evil is the hardest test most will face. Silence isn’t neutrality, it’s participation. Standing against injustice demands courage, even when it costs comfort or safety. Remember: doing nothing lets evil thrive. True strength is in choosing to act, not look away.

Eric Topol@erictopol.bsky.social · last yr.

Below, from earlier today, confirmed @statnews.com www.statnews.com/2025/04/18/n...

NIH said to have halted awarding of new grants to more top universities

Universities whose NIH funding has been frozen may face further strain as the agency holds off awarding new grants to at least a half dozen of them, according to an internal email.

statnews.com

Max Kozlov@maxkozlov.bsky.social · last yr.

Per source, NIH has been instructed to hold off from issuing ALL awards to Harvard, Cornell, Columbia, Brown, and Northwestern (including med schools) Agency staff have also been instructed to not speak about this funding freeze to grantees and applicants