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... --- #proteomics #prot-paper

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

A unified pan-cancer proteome atlas www.cell.com/cancer-... --- #proteomics #prot-paper

#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.... --- #proteomics #prot-paper

⏰ 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❗

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

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...

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...

nature.com

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... --- #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

Evosep @evosep.bsky.social · last yr.

#Immunopeptidomics combines #proteomics and #immunology to study the complex repertoire of peptides presented by major histocompatibility complex (MHC) molecules on the cell surface. Join our webinar exploring the topic on April 24 here: www.evosep.com/webinars/web... #teammassspec

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....

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...

analyticalsciencejournals.onlinelibrary.wiley.com

🚀 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/...

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.

pubs.acs.org

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...

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.

nature.com

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

Congratulations to David for being a finalist for the YPIC #proteomics Fund! We are happy to support his application at the Immunopeptidomics Platform HI-TRON and hope the fund will make this breakthrough project possible in collab with David from @lukasbunse.bsky.social lab at @dkfz.bsky.social

@ypic.bsky.social · last yr.

Meet YPIC Student Proteomics Fund finalist David Palmero Cantón! David is a biotechnologist by training who specialized in cancer research during his master’s studies and is now pursuing his PhD at DKFZ-German Cancer Research Center.

News in Proteomics Research blog post | Finally! A comparison of different modalities for plasma proteomics! proteomicsnews.blogs... --- #proteomics #prot-other

Congratulations to the SPF finalists! At the Immunopeptidomics Platform at HI-TRON @dkfz.bsky.social, we are very happy to support David Palmero Canton. His commitment to his project and interest in learning more about #immunopeptidomics are exemplary

@ypic.bsky.social · last yr.

Here they are! 🥳 We are happy to announce the three SPF finalists who will accompany us in Athens. We will have the chance to learn more about their outstanding proteomics project ideas during the 2nd APG and congratulate one of them on winning a 5000€ grant to make that project come true!🤩

Hey #TeamMassSpec & #Proteomics Just like the past years, we, led by Dr. Christina Ludwig, are part of the organization of the amazing Brixen Proteomics Summer School. The first announcement is going on since a couple of days and many more exciting news will follow again soon.

Shabaz Lab@shabazlab.bsky.social · 2y ago

The Brixen Summer School is back and is, as usual, building up a strong speaker list. Thank you @eupaproteomics.bsky.social @ukbspr.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support!

DIA-NN 2.0 is released! We consider it the biggest step forward in the history of DIA-NN. On modern LC-MS almost all identifications are now peptidoform-confident, with major improvements e.g. for phospho. Some other cool things too: github.com/vdemichev/Di...

Release DIA-NN 2.0 · vdemichev/DiaNN

We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

github.com

The EuPA proteomics awards committee invites you to apply for six 2024 EuPA awards that will be handed out personally at #EuPA2025 congress in Saint-Malo, France. 🥳 Deadline for applying is February 14! Here you can find the links to the application forms: eupa.org/2024-eupa-aw...