Jason Derks

221 posts

Jason Derks

Jason Derks

@_JasonDerks

Increasing throughput of proteomics @ParallelSqTech

Boston, MA Katılım Aralık 2018
305 Takip Edilen244 Takipçiler
Jason Derks
Jason Derks@_JasonDerks·
Vimentin in Fibroblast cells is likely functionally analogous to Krt5 in Basal cells. It’s amazing that single cell proteomics can enable these types of finding. Check out the work from @_AndrewLeduc for more details!
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Andrew Leduc@_AndrewLeduc

The big one is finally out!! In this paper, we set out to provide insight into the fundamental question; How do the individual cells from complex tissues regulate their proteomes? Brief summary of our findings 👇 biorxiv.org/content/10.110…

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Julia Bauman
Julia Bauman@JuliaBauman2·
I was super excited to learn from @NikoMcCarty's essay, "How to Scale Proteomics", that there's an FRO working on high-throughput single-cell proteomics (@ParallelSqTech), and even more excited to see the progress they've made in just 2 years via their preprints. So here's a video about it! And some links you should check out⬇️
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Parallel Squared Technology Institute (PTI)
PTI will be represented at #ASMS2025 with with two posters (TP203 and ThP 533) and two talks (TOA 2:30 pm and WOA 8:30 am). Find us to hear about our PSMtag, and applications in Alzheimer's and aging biology!
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Prof. Nikolai Slavov
Prof. Nikolai Slavov@slavov_n·
We just released JMod: an open source software supporting multiplexed DIA. It supports parallelization in both the mass domain (plexDIA) using small mass offsets and in the time domain (timePlex). It enabled 27-plex DIA & much further scaling 🚀 biorxiv.org/content/10.110…
Prof. Nikolai Slavov tweet mediaProf. Nikolai Slavov tweet media
Parallel Squared Technology Institute (PTI)@ParallelSqTech

Increasing throughput in mass spec proteomics requires new ways to model the increased complexity of the spectra. To model highly multiplexed mass spectra, we developed JMod. JMod enables new multiplexing approaches in the time and mass domains. biorxiv.org/content/10.110…

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Jason Derks
Jason Derks@_JasonDerks·
This work was a collective effort by members of @ParallelSqTech, enabled analytically through the development of specialized search software (JMod) and through mass-tag engineering (PSMtag).
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Jason Derks
Jason Derks@_JasonDerks·
We are excited to introduce ‘time’ as a new domain for proteomics multiplexing! It enables: -Label-free multiplexing -Combinatorial multiplexing with plexDIA Using 9-plexDIA and 3-timePlex together we demonstrate 27-plex DIA 🚀 biorxiv.org/content/10.110…
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Andrew Leduc
Andrew Leduc@_AndrewLeduc·
Our paper on the impact of protein leakage due to loss of membrane integrity for single cell proteomic sample prep is out in @NatureComms! We analyze thousands of primary single cells from murine tracheal tissue and record membrane permeability🧵 nature.com/articles/s4146…
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Vadim Demichev
Vadim Demichev@DemichevLab·
We have released DIA-NN 2.1.0, download link github.com/vdemichev/DiaN…, release notes github.com/vdemichev/DiaN…. It is a minor update, main highlights are: - Built-in support for Thermo .raw (Windows + Linux) - New QC metrics in PDF report & visualising trends across the experiment
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Slavov Laboratory
Slavov Laboratory@slavovLab·
We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. biorxiv.org/content/10.110…
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Andrew Leduc
Andrew Leduc@_AndrewLeduc·
Check out our work on identifying and providing solutions for protein leakage artifacts associated with sample preparation. It all started out with our struggle to explain a strange bi-clustering pattern in our data.
Slavov Laboratory@slavovLab

A new preprint: While analyzing proteomes of cells from mammalian tissues, @_AndrewLeduc identified protein leakage from permeabilized cells. We identified clear patterns that can be used to detect & mitigate this issue: biorxiv.org/content/10.110…

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Slavov Laboratory
Slavov Laboratory@slavovLab·
A new preprint: While analyzing proteomes of cells from mammalian tissues, @_AndrewLeduc identified protein leakage from permeabilized cells. We identified clear patterns that can be used to detect & mitigate this issue: biorxiv.org/content/10.110…
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