iiinova — where your digital self keeps evolving

Juan Camilo Rojas E. @juank1892.bsky.social · 01/07/2025

Had a great time at the GLYCOSCIENCE NL 2025 meeting last Friday—diverse and fascinating glycosylation topics. I also shared a sneak peek of work with the brilliant Nika Šimičić and Noortje de Haan. More soon—stay tuned for our cell-surface glycoproteome study in colorectal cancer cell lines!

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Juan Camilo Rojas E. @juank1892.bsky.social · 01/07/2025

Thank you very much @sinzandrea.bsky.social ! It was a pleasure to have you at my PhD defense! Thank you for your support through the finishing steps of this cycle! Looking forward to the new cool things this mass spec nerd can get its hands on :)

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Juan Camilo Rojas E. @juank1892.bsky.social · 16/06/2025

Most carbonylation sites were observed in human serum albumin (HSA) at few modification hotspots, showing selectivity in modification and alluding to the antioxidant potential of HSA. Deeper proteome coverage will have to be achieved by exploring depletion techniques in the future.

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Juan Camilo Rojas E. @juank1892.bsky.social · 16/06/2025

No significant differences were found with respect to site abundance in between healthy individuals and patients diagnosed with rheumatoid arthritis. However, these PTMs could be detected in the majority of donors, highlighting an important milestone in the robust detection of protein carbonylation.

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Juan Camilo Rojas E. @juank1892.bsky.social · 16/06/2025

The combined used of IMS, DDA, DIA, and peptide centrict analysis with Skyline was essential for robust detection and discovery of unknown carbonylation products. All filtered Skyline documents and MS data can be found in: panoramaweb.org/HumanSerumCa...

panoramaweb.org

Panorama Dashboard: /Panorama Public/2024/U of Leipzig AG Bioanalytics - Carbonylation in Rheumatoid Arthritis

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Juan Camilo Rojas E. @juank1892.bsky.social · 16/06/2025

Happy to finally share my last contribution of my PhD work on protein carbonylation. These diverse and low abundant non-enzymatic PTMs have strong implications in protein structure. Here we show how we managed to consistently detect them in serum of 68 individuals. pubs.acs.org/doi/10.1021/...

pubs.acs.org

Screening of Protein Carbonylation Sites in Human Serum by Ion Mobility Mass Spectrometry

Excessive oxidative stress, associated with various diseases, can induce protein carbonylation-nonenzymatic modifications involving aldehyde or keto group formation. These modifications are structural...

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Reposted by Juan Camilo Rojas E.

Lindsay K Pino @lindsaykpino.com · 02/06/2025

Come on down! Two posters for the price of one! MP224/225 to get an overview of the @talusbio.bsky.social transcription factor atlas with Daniele Canzani and a vignette of applying the platform to mechanism of action studies with Julia Robbins. #ASMS2025

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Alexey Nesvizhskii @nesvilab.bsky.social · 15/05/2025

If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.

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Reposted by Juan Camilo Rojas E.

Chris Ashwood @cashwood.proteaglyco.com · 28/04/2025

Beyond the 2025 Letters of Support for Skyline: skyline.ms/project/home... As a consultant, it’s easy to recommend an MS vendor that contributes to Skyline. Currently: Agilent, Bruker, Sciex, Shimadzu, Thermo, and Waters Their support ensures that there is a vendor-neutral data analysis option.

skyline.ms

Start Page: /home/software/Skyline/funding/2025 LOS

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US HUPO @us-hupo.org · 16/04/2025

Check out our upcoming webinar! In this US HUPO X ABRF crossover event, you'll learn about where AI is currently used in proteomics and where it may be transformative in the future. Register now: ow.ly/tKB750VB1PN 🧪

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Reposted by Juan Camilo Rojas E.

Olga Vitek @olgavitek.bsky.social · 15/04/2025

A few more spots are still open for some of the in-person programs at May Institute on Computation and Statistics for Mass Spectrometry and Proteomics on April 28 – May 11, 2025 on the campus of Northeastern University in Boston MA computationalproteomics.khoury.northeastern.edu

computationalproteomics.khoury.northeastern.edu

May Institute – Computation and statistics for mass spectrometry and proteomics

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Chris Ashwood @cashwood.proteaglyco.com · 15/04/2025

I’m running a Skyline metabolomics “bite” as part of the UC Davis Bits and Bites series. It covers four tutorials and is a great way to immerse yourself into Skyline. 24th April, 9 am - 1 pm PT. $175. Covers QQQ, high res, cal curves, and CE optimisation. metabolomics.ucdavis.edu/bits-bites--03

metabolomics.ucdavis.edu

Bits & Bites # 03

Bits & Bites # 03: Skyline: Getting Started with Targeted Metabolomics Data ProcessingDate & Time: April 24, 2025, from 9 am to 1 pm PTInstructor: Dr. Christopher Ashwood, Protea GlycosciencesRegistra...

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Magnus Palmblad @magnuspalmblad.bsky.social · 19/02/2025

Do you have a passion for research software and believe in the power of Open Science to drive advancements in healthcare? If so, we are looking for you! www.lumc.nl/en/about-lum...

lumc.nl

Research Software Trainer | LUMC

Do you have a passion for research software and believe in the power of Open Science to drive advancements in healthcare? As a Research Software Trainer at LUMC, you contribute to expanding training c...

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Reposted by Juan Camilo Rojas E.

Brett Phinney @ucdproteomics.bsky.social · 29/01/2025

If you're looking at peptide differential expression. Skyline is insanely powerful , especially how it seamlessly calculates peak areas across different conditions and makes heatmaps and volcano plots

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Juan Camilo Rojas E. @juank1892.bsky.social · 11/12/2024

I would bet on MZmine for performance (I keep postponing getting to it). But the biggest challenge might be the learning curve and requirement of scripting to combine output with IDs (e.g. proteomics applications).

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