#Cellzome #TeamMassSpec opinions are my own
Heidelberg
Joined September 2021
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Michael Steidel retweeted
We 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!
In the interest of a fair comparison, we intentionally made it unfair.
Orbitrap-TMT vs. timsTOF-diaPASEF across Kinobeads and 2D-TPP.
analyticalsciencejournals.on…
#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?
Michael Steidel retweeted
We are delighted to present DIA-NN 2.5. Redefining LC-MS proteomics with up to 70% more proteins identified and powerful capabilities for statistics, visualisation and biological interpretation.
Hey #TeamMassSpec
Proteomics Ruler question: there doesn’t seem to be a clear, explicit reference on what exactly to include.
Should the ruler be based on core histones only (H2A/B, H3, H4), or also include H1 (linker histones) - or even more?
Any solid references?
Michael Steidel retweeted
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides.
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. biorxiv.org/content/10.1101/…
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. #proteomics #uniprot
By the way.. 43% of current TREMBL entries will be dropped soon anyway insideuniprot.blogspot.com/2…
Michael Steidel retweeted
A simple benchmark.
Most people can understand it.
No PhD-level intelligence needed.
Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run.
biorxiv.org/content/10.1101/…
#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?
nature.com/articles/s41592-0…
Michael Steidel retweeted
Protein digestion in 200 nL on solid-phase tips: SPEC enables low-input proteomics—even with SDS/SDC at high levels. From FFPE and muscle to high throughput plasma. SPEC is a universal and Evosep-compatible protocol.
biorxiv.org/content/10.1101/…
biorxiv.org/content/10.1101/…
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.
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/acs…
Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024:
Michael Steidel retweeted
DIA-NN support for PAMAF (MOBILion): In proteomics, can we direct all peptide ions to fragmentation, therefore maximising sensitivity?
We have previously introduced Slice-PASEF as a method of choice for single-cell level sample amounts. But what is the full potential of this idea, if combined with high-resolution ion mobility separation?
We are excited to announce that we now have a preliminary implementation of PAMAF support in DIA-NN (Parallel Accumulation with Mobility Aligned Fragmentation, MOBILion), with some very promising first results.
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!
pubs.acs.org/doi/10.1021/acs…
