Hi #TeamMassSpec, Anyone out there already using EvoSep LUPO? First impressions?
Michael Steidel
@michaelsteidel.bsky.social
#Cellzome #TeamMassSpec #Proteomics opinions are my own
We preprinted a method of measuring phosphosite stoichimetries (occupancies) in just two mass spectrometry acquisitions, using internal stable isotope labelled controls.
www.linkedin.com/posts/nico-z...
Research Scientist – Proteomics Workflow Innovation (m/f/d) in Heidelberg, Germany | GSK Careers | Nico Zinn
🚀 We’re hiring in Omics Science and Technology at Cellzome / GSK (Heidelberg)! Excited to share that we have two open roles in Proteomics & Metabolomics. We’re looking for talented scientists who want...
linkedin.com
#TeamMassSpec: any independent data on dual-column LC creating subtle batch effects in LFQ proteomics? Thinking column A/B intensity shifts, missingness, RT drift, or condition-column confounding. Vendor claims are nice; real-world datasets would be nicer.
#TeamMassSpec Has anyone actually done a clean head-to-head comparison of TMT quant on AstralZoom-Orbi vs TOF?
Single-molecule peptide sequencing through reverse translation of peptides into DNA www.nature.com/artic... --- #proteomics #prot-paper
A Ground-truth validation of FDR & false localisation control in proteomics – a must-read from Stefan Tenzer’s lab! The benchmarks are quite enlightening. We are pleased to see our DIA-NN 2.0 excelling in sensitivity - often by a wide margin - while controlling FDR and false localisation rates.
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: One-Pot Dephosphorylation for Rapid and Sensitive Analysis of DIA Phosphoproteomics Data. Now out in Analytical Chemistry! Makes predicted phosphopeptide libraries 10x-20x smaller. Link below.
Proteomic Ruler question: In Wiśniewski et al., MCP 2014, the histone→DNA proxy seems implicit. Is there any explicit reference stating that the Ruler uses only core histones (H2A/H2B/H3/H4) and excludes H1? #proteomics #massspec
Bonus, info about DIA multiplex tags, up to 30-plex: "trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to increase these to beyond 30"
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics www.nature.com/articles/s41...
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications
Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...
nature.com
Hey #TeamMassSpec, Many non-human proteomics studies still search against taxon-filtered FASTAs. ❌ Redundant sequences ❌ Inflated search space ✅ Reference proteomes cut redundancy, improve annotation, and make results comparable. 👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot
Without #2, a lower ion count is needed just to be sure that the full MS range is scanned, but with more accurate ion counts, you can go to the max S/N without losing ions on the edges. This could also work for the Orbitrap Astral. Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...
With 𝗗𝗜𝗔-𝗡𝗡 𝟮.𝟯.𝟬 Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: github.com/vdemichev/Di...
Hey #TeamMassSpec, When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer? Taxonomy-filtered UniProt (all entries) Reference proteome (SwissProt+TrEMBL) Ensembl/GENCODE Something else?
Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run. www.biorxiv.org/content/10.1...
DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before: github.com/pwilmart/qua...
GitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies
Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison
github.com
#TeamMassSpec, Any opinions on why not generally adding the relatively small yeast proteome to the anyway large human search space (*.fasta) as an internal FDR quality control? www.nature.com/articles/s41...
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods
A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...
nature.com
The videos from the 8th Single-Cell Proteomics Conference (#SCP2025) will be joining this growing YouTube playlist. www.youtube.com/playlist?lis...
Hi #TeamMassSpec #EvoSep – Anyone using WhisperZoom for standard inputs (~500 ng)? Getting great data on timsTOF Pro Ultra (with ICC2), but repeatedly hit overpressure on Aurora columns - forcing me to discard them. Anyone else seeing this?
www.biorxiv.org/content/10.1... SPEC :The better SP3?
A Solid-Phase Extraction Capture (SPEC) workflow in nanoliter volumes for fast, robust and ultrasensitive proteomics
Despite great progress, sample preparation remains an area for improvement in proteomics, particularly for low-input samples where conventional protocols lead to losses and incomplete digestion. We pr...
biorxiv.org
Introducing the new timsMetabo! A metabolomics focused timsTOF: - enhanced ion capacity of the dual-stage TIMS-MX ion funnel - Athen Ion Processor-equipped timsMetabo, up to 300 Hz PRM Also QSee software (a nightmare at talks, QC or Qsee?). As found by Biswapriya Misra www.bruker.com/en/news-and-...
www.biorxiv.org/content/10.1... timePlex enables time-domain sample multiplexing in LC-MS — boosting proteomics throughput up to 9× with no labels and minimal compromise in quant accuracy. Combine with plexDIA for 27 samples/run.
Increasing mass spectrometry throughput using time-encoded sample multiplexing
Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate at which samples can be analyzed remains limiting. Throughp...
biorxiv.org
I am excited to see our performance assessment of the successor of Scanning SWATH on the Zeno TOF7600+ mass spectrometer - ZT Scan DIA - pre-printed (www.biorxiv.org/content/10.1...
Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput
Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in p...
biorxiv.org
"when compared to DIA-NN, DIA-BERT demonstrated a 51% increase in protein identifications and 22% more peptide precursors" www.nature.com/articles/s41...
DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis - Nature Communications
Data-independent acquisition mass spectrometry (DIA-MS) has emerged as a key technology in quantitative proteomics. Here, the authors introduce DIA-BERT, a transformer model pre-trained on existing DI...
nature.com
Significant impact of consumable material and buffer composition for low-cell number proteomic sample preparation chemrxiv.org/engage/... --- #proteomics #prot-preprint
