We preprinted a method of measuring phosphosite stoichimetries (occupancies) in just two mass spectrometry acquisitions, using internal stable isotope labelled controls.

#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.

It's called the Agilent 6495D.

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...

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...

Sciex in the game. Pretty impressed by ScanningSWATH data on the new ZenoTOF 8600. #TeamMassSpec

#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...

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?

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.

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...

"when compared to DIA-NN, DIA-BERT demonstrated a 51% increase in protein identifications and 22% more peptide precursors" www.nature.com/articles/s41...

Significant impact of consumable material and buffer composition for low-cell number proteomic sample preparation chemrxiv.org/engage/... --- #proteomics #prot-preprint

Hey #TeamMassSpec #SingleCell #Proteomics, when using DDM in your workflow do you see it eluting from the column? If so at which m/z. Desperately looking for [M+H]+ at m/z 511.32

„Our method clusters peptides with similar quantitative behavior, providing a new approach to the protein grouping problem and enabling identification of regulated proteoforms directly from bottom-up data.“ www.biorxiv.org/content/10.1...

New #tidyplots cheatsheet 🤩 tidyplots.org/cheatsheet #rstats #dataviz #phd

Hi #TeamMassSpec, Does anyone have a clue how to assign multiple MS methods to single run via Bruker HyStar? pubs.acs.org/doi/10.1021/...

Protein IDs for early #PAMAF performance on an Agilent QTOF (fyi - not our final detector) #USHUPO

To those attending USHUPO: Is anyone willing to leak the absolute IDs in addition to the relative Mobilion IDs from the whitepaper? #TeamMassSpec #Proteomics #PAMAF

The Trump administration is so on top of things that scientists EXTERNALLY FUNDED BY INDUSTRY WHO MAKE THE HHS MONEY are receiving termination letters. These fucking morons have no idea how the government even works. AT ALL

Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024:

Calling all #TeamMassSpec experts. I’m planning to revisit the classic SCX fractionation protocol but ran into a challenge - I can’t find a vendor for syringes with metal springs to make stage tips. I’d be so grateful for any suggestions or advice you might have 🙏 *attaching picture as an example

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...

Weather’s going wild, and now your mass spec data’s a mess too? Coindidence? Nope! We reveal how weather-driven air pressure fluctuations impact diaPASEF-based high troughput proteomics - and how to fix it! Check out our new paper! #diaPASEF #Weatheromics pubs.acs.org/doi/10.1021/...

I am planning to switch from DDA to #DIA for our proteomics experiment on Orbitrap Exploris. Question: FAIMS yes or no? If I do not use FAIMS for library generation, can I use it for DIA measurements? Or the other way around? #massspectrometry #proteomics #teammassspec

🚀 Robust and high sensitivity #proteomics: Our Nature protocol demystifies #PASEF workflows and provides ready-to-use dia-PASEF & synchro-PASEF methods. Find out how to achieve 7,000 protein groups or 29,000 phosphosites in 21min. Let's explore! #TeamMassSpec #Bruker doi.org/10.1038/s415... 1/🧵

Hi #TeamMassSpec, Is it expected that diaPASEF file size triples from Pro2 to Ultra2? (From 2 GB to 6 GB, 60 SPD) ...

- Bruker did a full calibration remotely (didn't help) - I connected the CaptiveSpray Ultra to the other TimsTof Pro with the other nanoElute and the same effect so it is not the MS and not LC The problem is most probably in ITI or the whole CaptiveSpray source.

This may be an incredibly naive mass spec question, but what's a PSM for DIA data, particularly in Spectronaut? Is it simply referring to a confidently ID'd precursor?

Trying to estimate popularity of search engines. (Something widespread I missed out?) Based on citations/year of initial publication it seems as MSFragger would take over soon...

Hey #TeamMassSpec, Anyone there having both timsTOF SCP/Ultra + #OrbiTOF Astral in their lab? Would be interested in comparisons. Where do both have their respective sweet spots?

Anyone having a good explanation why all Orbi systems require frequent cleaning while timsTOFs just continue to run stable ?

Has anyone tried already cleaning-up proteins from Trizol samples using SP2/SP3/SP4 ? Acetone precipitation does not work robustly..

Hey # TeamMassSpec, Have you ever considered DIA for small pulldown studies? I know that should definitely be one of the TMT sweetspots, but have not seen any back-to-back comparison so far..