Jason Derks

Increasing throughput of proteomics @ParallelSqTech

[Jason Derks @_JasonDerks]

I’ll be attending iSCMS and presenting work from @ParallelSqTech. I look forward to sharing what we have been up to and learning from the community!

[Parallel Squared Technology Institute (PTI) @ParallelSqTech]

@_JasonDerks is presenting at iSCMS! Come by this Saturday afternoon around 2pm to hear his talk: "Increasing proteomics throughput by multiplexing in the mass and time domains".

https://t.co/IY8ztiXV1H

[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!

[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 👇
https://t.co/4dRXpGJTGn

[Andrew Leduc @_AndrewLeduc]

This work is the culmination of everything I have worked on since starting my PhD. 🧵

[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⬇️

[Parallel Squared Technology Institute (PTI) @ParallelSqTech]

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!

[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 🚀

https://t.co/u1I1QAZxSN

[Jason Derks @_JasonDerks]

Links to our preprints:

timePlex (multiplexing with time-offsets): https://t.co/tDeYgJuLei

JMod (search software for joint-modeling): https://t.co/HBOrxeiUGf

PSMtag (novel mass tag for 9-plexDIA): https://t.co/ei449lDkpr

[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 🚀
https://t.co/tDeYgJuLei

[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).

[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🧵
https://t.co/uj2Wpz8LRs

[Prof. Nikolai Slavov @slavov_n]

Protein samples can be multiplexed to increase throughput.

In 2023, @ParallelSqTech set out to make tags (barcodes) that not only increase throughput but also enhance peptide sequence identifications: https://t.co/RsZzKeWihh

We will share results soon: https://t.co/rJQ6PSkcmI

[Vadim Demichev @DemichevLab]

We have released DIA-NN 2.1.0, download link https://t.co/4x5BsyVfiC, release notes https://t.co/yTctBkcoVx.
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

[Jason Derks @_JasonDerks]

@erwinschoof @slavovLab I really enjoyed the conference! Thank you again for the invitation to present our work!

[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.

https://t.co/lAxvulC4zx

[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:

https://t.co/CSopooo47J