David Gomez-Zepeda

Trainees: If you haven't already, learn the value of implementing the Bat Signal with your peers. When you're stuck and need a body double, a review, a brainstorm, an escape... this can be game-changing. Don't worry about being a bother, instead: pay it forward. We all need it a some point. 1/3

Conventional proteomics searches struggle with many modifications and fully open searches may be difficult to interpret. We introduce a "detailed" mass offset search in #MSFragger boosting interpretability and localization especially in complex cases (e.g. FPOP data): www.biorxiv.org/content/10.1...

An automated workflow to address proteome complexity and the large search space problem in proteomics and HLA-I immunopeptidomics www.sciencedirect.co...

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#proteomics #prot-paper

A perspective on integrating digital pathology, proteomics, clinical data and AI analytics in cancer research www.sciencedirect.co...

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#proteomics #prot-paper

Some people seem to like the Bravo AssayMap, which has enrichment protocols using their proprietary cartridges and also autoSP3. There are several protocols using the Opentrons 2, but they aren't necessarily directly transferable compatible with the OT Flex, which also requires special tips.

A unified pan-cancer proteome atlas www.cell.com/cancer-...

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#proteomics #prot-paper

I had the opportunity to present MAETi, which enables #immunopeptidomics profiling of 10,000 cells. I was very happy to see that there is a lot of interest on it since @julbeyr.bsky.social , PhD student at Stefan Tenzer lab, has done a lot of great work optimizing it to reach these levels.

Megan Ford did an excellent job presenting our antibody-based workflow for high-throughput #immunopeptidomics of low-input cell and clinical samples. A big thanks to @dgpf.bsky.social sponsoring her travel award that made her assistance possible.

It felt like a big milestone to come back to France to present our work at the Immunopeptidomics Platform and Tenzer Lab HI-TRON Mainz, 7.5 years after my PhD in Paris:

Thanks a lot to the organizers and all the people who made it such a great experience. Merci beaucoup!
EuPA, FPS, and @ypic.bsky.social

#EuPA2025 was a blast !
Science was excellent and the personal discussions enriching. I was charmed to reconnect with the French proteomics community, and the breeze and beauty of Saint Malo made it unforgettable.

#TeamMassSpec attending the #EuPA2025 conference, don’t miss the presentations from the Tenzer Lab and Immunopeptidomics Platform to learn more about our recent work on #immunopeptidomics, and high-throughput and clinical #proteomics. See you in the beautiful Saint Malo!

Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data pubs.acs.org/doi/10....

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#proteomics #prot-paper

Immunostaining of liver tissue.

⏰ Don’t miss the chance to apply for this postdoc opportunity in spatial & single-cell proteomics in our lab at Karolinska Institutet @ki.se ! Plenty of exciting resources and projects on mitochondria and metabolism. Deadline: May 5 👉 bit.ly/4jXTxSK #mitochondria #metabolism #singlecell

The #Brixen Summer School on Proteomics is back! Join us for an immersive week of cutting-edge proteomics education and vibrant scientific exchange. To find the full program, follow this link: www.brixenproteomics.org/program/ . ❗Deadline for registration is 19th of May❗

Terminator holding a mass spectrometer saying "hasta la oxoprolina baby"

News in Proteomics Research blog post | Attention freeloaders! Skyline needs your support! It takes 60s to sign this thing! proteomicsnews.blogs...

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#proteomics #prot-other

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

Deep Visual Proteomics maps proteotoxicity in a genetic liver disease - Nature High-resolution spatial proteomics were used to map molecular events during hepatocyte stress in pseudotime across all fibrosis stages, recapitulating known disease progression markers and revealing e...

Our paper is out in Nature today! We use Deep Visual Proteomics (DVP) to dissect α1-antitrypsin deficiency (AATD) in human liver at single-cell resolution.
Let us take a tour through proteotoxic stress in intact human tissue — one hepatocyte at a time.
www.nature.com/articles/s41...

Job alert: fully funded postdoc position in chemical biology in beautiful Geneva! Do you have a PhD in Chemical Biology or related field with organic synthetic experience? Apply now! Details on how to apply can be found here: www.hoogendoornlab.org/joinus #chemsky #ChemBio

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search www.nature.com/artic...

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#proteomics #prot-paper

If you want to learn how to do #immunopeptidomics from <50,000 cells, join us at this Evosep webinar. @julbeyr.bsky.social will present Mild Acid Elution in a Tip (MAETi), a simple, antibody-free approach enabling unprecedented sensitivity

It depends on several factors: main application, budget, availability of service engineers in your region. Are your samples scarce? Do you aim for high-throughput? Mostly cell/tissue lysates or also plasma? Only proteomics or also peptidomics?

Rapid Determination of Isotopic Purity of Stable Isotope (D, 15N, or 13C)‐Labeled Organic Compounds by Electrospray Ionization‐High‐Resolution Mass Spectrometry Rationale Stable isotope-labeled organic compounds, containing D, 15N, or 13C, have widespread applications in chemistry, biology, environmental science, and agriculture. However, the isotopic purit...

Rapid Determination of Isotopic Purity of Stable Isotope (D, 15N, or 13C)-Labeled Organic Compounds by Electrospray Ionization-High-Resolution Mass Spectrometry #RCM analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10....

If 21k UP is consensus while 63k UP includes isoforms, the redundancy in the latter may result in lower cut-off.
I guess that >100 AAs includes 21k UP while the others include 63k UP. If that's the case, I do see the upwards trend.
Note aside, I would plot cut-off (dependent variable) in y axis

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected with Listeria monocytogenes were searched by four different search engines, PEAKS, Comet, Sage and MSFragger, followed by data-driven rescoring with MS2Rescore. Compared with individual search engine results, this integrated workflow boosted immunopeptide identification by an average of 27% and led to the high-confidence detection of 18 additional bacterial peptides (+27%) matching 15 different Listeria proteins (+36%). Despite the strong agreement between the search engines, a small number of spectra (<1%) had ambiguous matches to multiple peptides and were excluded to ensure high-confidence identifications. Finally, we demonstrate our workflow with sensitive timsTOF SCP data acquisition and find that rescoring, now with inclusion of ion mobility features, identifies 76% more peptides compared to Q Exactive HF acquisition. Together, our results demonstrate how integration of multiple search engine results along with data-driven rescoring maximizes immunopeptide identification, boosting the detection of high-confidence bacterial epitopes for vaccine development.

🚀 Boosting bacterial immunopeptide discovery! Our bioinformatics workflow integrates 4 search engines with follow-up rescoring to enhance ID by 27%, maximizing the discovery of vaccine candidates. Applied to timsTOF/Thermo data🦠💉Great work by Patrick Willems.

pubs.acs.org/doi/10.1021/...

I took a very basic MS course during my studies. A lot of self learning from books and publications, and by doing it since I was the only one doing proteomics at the lab where I did my PhD. Two summer schools were essential:
EMBO Targeted Proteomics Barcelona and European Advanced Proteomics Brixen

Mass-spectrometry-based proteomics: from single cells to clinical applications - Nature This Review summarizes advances in mass-spectrometry-based proteomics and explores the potential applications of these technologies in the clinic.

In our latest @Nature review with Tiannan Guo & Judith Steen, we explore how technological breakthroughs are revolutionizing MS-based proteomics: From enhanced sensitivity enabling single-cell analysis to high-throughput plasma proteomics & AI-based data interpretation
www.nature.com/articles/s41...

Enhancing tandem MS sensitivity and peptide identification via ion pre-accumulation in an Orbitrap mass spectrometer www.biorxiv.org/cont...

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#proteomics #prot-preprint

We want you on our team!

If you’re an expert in computational mass spectrometry, machine-learning-driven omics & high-throughput molecule identification, apply now for our tenure-track position at @univie.ac.at

jobs.univie.ac.at/job/Tenure-T...

#Hiring #MassSpec #Bioinformatics #Jobs