Robert Hardt

GitHub - MannLabs/pydiaid: An open-source Python package for dia-PASEF methods with Automated Isolation Design (py_diAID) from the Mann Labs at the Max Planck Institute of Biochemistry. An open-source Python package for dia-PASEF methods with Automated Isolation Design (py_diAID) from the Mann Labs at the Max Planck Institute of Biochemistry. - MannLabs/pydiaid

github.com/MannLabs/pyd...

My guess is that they used the tool from the Mann’s lab to optimize window placement to get the py-diaAiD PASEF method. Bit sketchy though.

So they made it public. Nice

Thanks for the prompt reply.

Was this done via unbiased shotgun LC-MS proteomics or target MS?

Yes. At least whenever I did a submission in PRIDE the data is initially always private. The author has to actively click a publish button and then is also asked to provide reference to the publication the data is linked to. Usually DOI.

The paper mentions that the raw data will be deposited under: JPST003404/PXD056519. Probably since it’s freshly accepted the authors just have not made it public yet.

Cell as Recycling center: Prof. Dr. Dominic Winter researches how it works. - Copyright © UDE / Anke Waelischmiler

#lysosomes, #massspectrometry...
weiterlesen

News in Proteomics Research blog post | pre-ASMS drops coming in! Seer system can prep 1,000 plasma proteomics samples/week! proteomicsnews.blogs...

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#proteomics #prot-other

Seer’s Proteograph Platform Enables Unprecedented 20,000-Sample Proteomics Study with Korea University to Develop AI-Driven Diagnostics for Cancers in Young Adults Seer (NASDAQ: SEER) and Korea University announced a groundbreaking 20,000-sample proteomics study to develop AI-driven cancer diagnostics for young adults. The three-year study, funded by Korea's K-Health MIRAE initiative, will analyze 15,000 cancer patients and 5,000 healthy controls using Seer's new Proteograph ONE Assay and SP200 Automation Instrument. The platform can process over 1,000 samples weekly, requiring only one mass spectrometry injection per sample and completing 80-sample batches in under 5 hours. The study leverages Seer's technology alongside Thermo Scientific's Orbitrap Astral mass spectrometer to identify up to 10 times more proteins than conventional methods. Samples will be sourced from leading Korean institutions including Seoul National University Hospital, National Cancer Center, and Samsung Medical Center. This collaboration aims to revolutionize early cancer detection and treatment in young adults through AI-powered diagnostics.

#SEER Seer’s Proteograph Platform Enables Unprecedented 20,000-Sample Proteomics Study with Korea University to Develop AI-Driven Diagnostics for Cancers in Young Adults

https://www.stocktitan.net/news/SEER/seer-s-proteograph-platform-enables-unprecedented-20-000-sample-j5bux0zunuwx.html

Same here. I used the unadjusted p-value for y-axis plotting in the Volcano but drew the cutoff line based on p adjust.

Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics pubs.acs.org/doi/10....

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#proteomics #prot-paper

Looks like he is following the same path other populist leaders like the Dutch guy Wilders have already done in the Netherlands. But I am not surprised. If you ignore science and the power of facts that’s where you end up. For those guys it seems scientific facts are just one of many opinions.

Where would genomics be if the BAM/SAM file format was proprietary and Bamtools/Bowtie was closed source and prohibitively expensive? That's where the proteomics field is right now. Talus Bio's @willfondrie.com and a group of industry+academia leaders share -

#proteomics #massspectrometry #DIA #PRM

resulting in an approach with both whole proteome coverage and high sensitivity for low abundant lysosomal hydrolases. Application for the analysis of a mouse model of metachromatic leukodystrohy resulted in exciting new insights in disease pathology. Check it out!

Data-Independent Acquisition–Parallel Reaction Monitoring Acquisition Reveals Age-Dependent Alterations of the Lysosomal Proteome in a Mouse Model of Metachromatic Leukodystrophy For the reproducible analysis of peptides by mass spectrometry-based proteomics, data-independent acquisition (DIA) and parallel/multiple reaction monitoring (PRM/MRM) deliver unrivalled performance with respect to sensitivity and reproducibility. Both approaches, however, come with distinct advantages and shortcomings. While DIA enables unbiased whole proteome analysis, it shows limitations with respect to dynamic range and the quantification of low-abundant proteins. PRM, on the other hand, is ideally suited to reproducibly quantify selected proteins even if they are low-abundant, but no knowledge of the remaining sample is obtained. Here, we combine both methods into a mixed DIA-PRM acquisition approach, merging their benefits while operating at reduced machine run times and needed sample amounts. We demonstrate the feasibility of DIA-PRM by merging a scheduled PRM assay for 103 peptides, representing 59 low-abundant lysosomal hydrolases, with a DIA data acquisition scheme. After benchmarking DIA-PRM with mouse embryonic fibroblast (MEF) whole cell lysates, we use the approach to investigate age-related proteomic changes in brain tissues of a mouse model of metachromatic leukodystrophy (MLD). This revealed an MLD-related progressive increase in distinct classes of lysosomal hydrolases as well as alterations of proteins related to myelin and cellular metabolism. All data are available via ProteomeXchange with PXD052313.

Reposting it here since my former boss hasn‘t done the move to Bluesky yet:

pubs.acs.org/doi/10.1021/...

New paper from our group in Analytical Chemistry. Anne Sanner with support from Robert Hardt devised an approach to combine DIA analyses and scheduled PRM assays,

You will need to ask for a free viewer only license which has to be renewed every year unfortunately.

I envy you. Also want one. 😜Would probably look also great as an ornament on the Christmas tree.

Congrats and all the best.

But even longer times it is quite stable. We are using IC calibration at the start of each run as well.

Roughly once a week.

Well the Bluebird honestly died when Leon took over…

I spend a bit of time talking to folk with plasma cohorts about MS vs affinity approaches for discovery. Thought it was worth a thread.

Most love the marketing. 5,000 proteins? 10,000 proteins? OLink was used in UK Biobank? Wow, mass spec is sooooo last year. Except life is not that simple.

Hi Lee. I could ask a friend of mine from the Netherlands who is a assistant prof in glycoproteomics. She is not on Bluesky yet though.

Why not? #science #Teammassspec

A flock of ‘rubber duck’ Christmas baubles

Debating getting a @chemjobber.bsky.social ornament for the Christmas tree this year…

Of course @lkpino.bsky.social instigates the first legit mass spec proteomics thread I’ve seen over here. Well done everyone! 👏

Also, next week see Lindsay et al. battle countless quant foes (not each other!) in the second US HUPO LFQ Battle Royale.

😱 I have just seen a photo from MSVision on LinkedIn! What a horror! I had once a catastrophic failure of the turbopump in LTQ Orbitrap, but not like THAT!

so, wir checken hier mal die Lage