Reposted by Michael SteidelVadim Demichev @vadim-demichev.bsky.social · 16/09/2026We have released DIA-NN 2.7. Performance improvements (more proteins) and GUI improvements. In particular, added a data completeness filter for pathway analysis. Further feedback on how to improve statistics and visualisation in DIA-NN is very welcome! 192
Michael Steidel @michaelsteidel.bsky.social · 16/09/2026In the interest of a fair comparison, we intentionally made it unfair. Orbitrap-TMT vs. timsTOF-diaPASEF across Kinobeads and 2D-TPP. analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...analyticalsciencejournals.onlinelibrary.wiley.comCross‐Platform Comparison of Chemoproteomics Workflows: Orbitrap‐TMT Versus timsTOF‐diaPASEFChemoproteomics aims to achieve precise and comprehensive quantification of protein–small molecule interactions, yet methodological comparisons across quantitative proteomics workflows remain scarce..... 030
Michael Steidel @michaelsteidel.bsky.social · 29/07/2026Hi #TeamMassSpec, Anyone out there already using EvoSep LUPO? First impressions? 000
Michael Steidel @michaelsteidel.bsky.social · 03/06/2026Very interesting work. Did you assess how robust the occupancy estimates remain at very low stoichiometries, e.g. below 5–10%, where the expected change after phosphatase treatment may approach normal quantification error? 110
Reposted by Michael SteidelVadim Demichev @vadim-demichev.bsky.social · 02/06/2026We preprinted a method of measuring phosphosite stoichimetries (occupancies) in just two mass spectrometry acquisitions, using internal stable isotope labelled controls. 1135
Michael Steidel @michaelsteidel.bsky.social · 30/05/2026reeserichardson.blog/2026/05/28/h...reeserichardson.blogHow much of Thermo Fisher’s antibody data has been manipulated?We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog 010
Michael Steidel @michaelsteidel.bsky.social · 28/05/2026www.linkedin.com/posts/nico-z...linkedin.comResearch 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... 011
Michael Steidel @michaelsteidel.bsky.social · 26/05/2026#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. 000
Michael Steidel @michaelsteidel.bsky.social · 21/05/2026Exactly! But my question is even narrower: on the same Astral Zoom instrument, has anyone directly compared TMT reporter quant from the Astral analyzer vs the Orbitrap? Your recent preprint uses TMT on Zoom, but I don’t see that clean head-to-head. 100
Michael Steidel @michaelsteidel.bsky.social · 21/05/2026Fair point - but which one is worse then: Orbitrap MS2-TMT or TOF MS2-TMT? 200
Michael Steidel @michaelsteidel.bsky.social · 21/05/2026#TeamMassSpec Has anyone actually done a clean head-to-head comparison of TMT quant on AstralZoom-Orbi vs TOF? 210
Reposted by Michael SteidelPastelBio @pastelbio.bsky.social · 19/03/2026Single-molecule peptide sequencing through reverse translation of peptides into DNA www.nature.com/artic... --- #proteomics #prot-paper 044
Reposted by Michael SteidelVadim Demichev @vadim-demichev.bsky.social · 12/03/2026A 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. 1194
Reposted by Michael SteidelVadim Demichev @vadim-demichev.bsky.social · 23/02/2026Solving 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. 1103
Michael Steidel @michaelsteidel.bsky.social · 03/01/2026Naive question: I thought targeted was about sensitivity - why ng? 120
Reposted by Michael SteidelChris Ashwood @cashwood.proteaglyco.com · 03/01/2026It's called the Agilent 6495D. 151
Michael Steidel @michaelsteidel.bsky.social · 27/12/2025Not a conference, but worth flagging: EMBO Practical Course “Targeted proteomics: advanced tools for biomedical research” Barcelona, 8–13 Nov 2026 Line-up not announced yet, but previous editions organized by @maccoss.bsky.social with invited speakers incl. Alexey Nesvizhskii and Vadim Demichev. 151
Michael Steidel @michaelsteidel.bsky.social · 14/12/2025Proteomic 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 022
Michael Steidel @michaelsteidel.bsky.social · 07/12/2025I agree MaxLFQ isn’t meant for absolute quantification. But that still doesn’t explain the complete lack of correlation with UPS2. From my experience, iBAQ and MaxLFQ usually correlate well (R² ~0.78, non related example dataset shown), suggesting they track the same MS1 signal. 110
Michael Steidel @michaelsteidel.bsky.social · 06/12/2025As shown in the DIA-NN paper, the mobility term contributes only negligibly to the discriminant score, suggesting that measured CCS -even with good IM resolution - might simply be too affected by gas-phase ion–ion / ion–neutral interactions to provide a stable, high-specificity constraint … 040
Michael Steidel @michaelsteidel.bsky.social · 06/12/2025With a quadrupole we know exactly which precursor m/z window was isolated -the precursor mass is tightly defined with a well-characterised error. My question was whether CCS can provide anything close to that level of search-space restriction for database searching. 120
Michael Steidel @michaelsteidel.bsky.social · 06/12/2025My point rather was whether precursor CCS can actually constrain the search space during database searching not just what Da-equivalent tolerance it has. 110
Michael Steidel @michaelsteidel.bsky.social · 06/12/2025Asking for a friend: Is intrinsic specificity of CCS high enough to serve as an effective in silico precursor filter during database searching? 130
Michael Steidel @michaelsteidel.bsky.social · 20/11/2025“Very interesting! Do you know whether ProteomeSciences is already testing the new DXT tags with selected customers or collaborators, or is it still entirely in-house at this stage?” 110
Reposted by Michael SteidelChris Ashwood @cashwood.proteaglyco.com · 18/11/2025Bonus, 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" 121
Reposted by Michael SteidelMichael MacCoss @maccoss.bsky.social · 06/11/2025Fantastic 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...nature.comCarafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature CommunicationsAccurate 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... 03810
Michael Steidel @michaelsteidel.bsky.social · 07/10/2025Surprised that u go so low. With EvoSep 24 min method we can load lots more on our Ultra2 until reaching saturation especially with ICC2.0 100
Michael Steidel @michaelsteidel.bsky.social · 07/10/2025How much are you loading per injection? Is ICC 2.0 enabled on the Ultra2? And which library are you using? 110
Michael Steidel @michaelsteidel.bsky.social · 02/10/2025True — but the odd part is that the Human Reference Proteome is not really ‘canonical only’. Non-canonical entries from TrEMBL are included, yet the curated SwissProt isoforms are missing default. That’s what undermines the idea of a high-quality reference set. 100
Michael Steidel @michaelsteidel.bsky.social · 01/10/2025On a separate note: I was surprised to find that none of the non-canonical SwissProt isoforms are included in the official human reference proteome (UP000005640). Anyone know what’s going on here? 🤔 #proteomics #bioinformatics @pwilmarth.bsky.social il 220
Michael Steidel @michaelsteidel.bsky.social · 30/09/2025By the way.. 43% of current TREMBL entries will be dropped soon anyway insideuniprot.blogspot.com/2025/06/capt...insideuniprot.blogspot.comCapturing the Diversity of Life - Reorganizing the Protein Space in UniProtKBAdvances in genome sequencing technology means that large-scale efforts such as the Earth Biogenome project and the Darwin Tree of Life ... 220
Michael Steidel @michaelsteidel.bsky.social · 30/09/2025Hey #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 292
Reposted by Michael SteidelChris Ashwood @cashwood.proteaglyco.com · 28/09/2025Without #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... 282
Reposted by Michael SteidelVadim Demichev @vadim-demichev.bsky.social · 26/09/2025With 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... 3296
Michael Steidel @michaelsteidel.bsky.social · 25/09/2025Thanks @pwilmarth.bsky.social - also included the less-redundant "one protein per gene" db here ...Has anybody assessed potential benefits of the reduced search space on sensitivity? 220
Michael Steidel @michaelsteidel.bsky.social · 25/09/2025Great thanks! Where can I find the one protein per gene option? 200
Michael Steidel @michaelsteidel.bsky.social · 25/09/2025Hey #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? 140
Michael Steidel @michaelsteidel.bsky.social · 19/07/2025Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run. www.biorxiv.org/content/10.1... 050
Reposted by Michael SteidelPhil W @pwilmarth.bsky.social · 04/07/2025DIA, 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.comGitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studiesComparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison 34113
Michael Steidel @michaelsteidel.bsky.social · 27/06/2025Sciex in the game. Pretty impressed by ScanningSWATH data on the new ZenoTOF 8600. #TeamMassSpec 1112
Michael Steidel @michaelsteidel.bsky.social · 25/06/2025Using 32-Core Threadripper for DIA-NN. Gamechanger for large studies as multithreading is efficiently used. Also in case if several user need to process different jobs at same time. 010
Michael Steidel @michaelsteidel.bsky.social · 24/06/2025If I got that correctly its not „truly“ open, as only predefined offset masses can be selected. Have tried Fragpipe22? You can do ion mining from DIA data … 330
Michael Steidel @michaelsteidel.bsky.social · 24/06/2025..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment) 110
Michael Steidel @michaelsteidel.bsky.social · 23/06/2025#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...nature.comAssessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature MethodsA 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... 130
