Michael Steidel

Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run.

www.biorxiv.org/content/10.1...

Is that narrow windowed thin-PASEF?

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

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

Using 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.

If 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 …

Sure. Why?

..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment)

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...

#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...

Aurora Elite™ CSI 15x75 C18 UHPLC column - IonOpticks 15 cm x 75 μm C18 UHPLC packed emitter column, compatible with all Bruker CaptiveSpray sources.

Aurora Elite CSI 15cmx75um. Unfortunately EvoSep methods cannot be modified..

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?

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...

www.biorxiv.org/content/10.1...

SPEC :The better SP3?

Is that related to timePlex?

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-...

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...

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.

Thanks Chris!

When they say “Mass Spectroscopy,” somewhere an Orbitrap detector quietly dies.

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...

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...

Unfortunately no diaPASEF support at the moment..

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...

"when compared to DIA-NN, DIA-BERT demonstrated a 51% increase in protein identifications and 22% more peptide precursors"

www.nature.com/articles/s41...

#PipetocalypseNow

Anyone tried low amounts of DMSO for EvoSep buffers?

Not tested so far. Tried these?

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

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#proteomics #prot-preprint

Which does not necessarily exclude accumulation in the TIMS funnel causing space charge effects -> ion supression

Thanks! Unfortunately no indication for 1021.62 from my EvoSep data. In addition not sure how this m/z fits to MW of 510.6

Slice-PASEF: Almost as beautiful as gazing into the starry sky at night