Matthew Russell

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.

I'm a huge fan of this proposal!

If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data?

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

My latests was two tables in separate formats in two separate word documents and an extra column of data in free text in an email.
But it was a tiny data set describing metadata, and the colaborator is lovely and it's all good.

Totally.

Love that. Very pithy way of pointing out we don't need to build a fusion reactor because we've got one, we just need some solar cells to get electrisity from it.

which is why this as an identity not a prerequisite relationship: it's the code that realizes your thoughts about a problem's structure and solution. Sometimes those are creative, novel, even inspiring thoughts (sometimes not), but when your brain turns to lunch, those thoughts are still there.

There is a position open in our lab, within this network. Our project deals with assessing identification and quantification errors for MS-based proteomics. www.protaiomics.eu/project/dc13...
Please check out all the project descriptions at the site below:

I love the science - art interface stuff and @irinabezsonova.bsky.social drawings are really cool.

I just love cutaway images of mass spectrometers, and mini mass spectrometers are always just the cutest.

Thinking about it, that is actually possible in my case also. That is weird isn't it.

Ah, OS level and not inside positron. Thanks, I'll give it a try.

Agree on sympathy for devs! I seem to have to restart the whole PC to deal with it, which is a bit trick on a remote PC running other long data procesing jobs!

Tantalsing tip. I can't find where that seeting would be. I tried changing quarto language to en_us, but that didn't change the ctrl-c problem. How do I get to the language setting you mean?

Keyboard shortcut for "Copy" fails randomly · Issue #9364 · posit-dev/positron System details: Mac Positron and OS details: Mac is running Sequoia 15.6.1. Positron Version: 2025.08.0 build 130 Code - OSS Version: 1.102.0 Commit: 76ddce5 Date: 2025-08-01T20:08:51.894Z Electron...

My #positron has stopped recognising ctrl-c copy; 90% of my #rstats workflow is ctrol-c -> ctrl-v -> edit code. Looks like it's a known bug in VScode that will get fixed, but man, that is a weirdly specific and devistating bug.

github.com/posit-dev/po...

So much this.

caught between getting students to use R on University computer lab machines (systematically cursed by Uni IT in a different way every semester) or bringing their own laptop (always a few uniquely cursed and dysfunctional)

That looks really intersing. Are you using the micro S-trap rather than the plate? I generally thought the plate would be easier to automate.

Bluesky needs a count bookmarks feature, so I can see how many articles and posts I wanted to come back to and re-read and follow up on, and probably never will.

Strong "know to be useful or believe to be beautiful"* vibes.

* Famous paraphrased quote of William Morris.

How about base R:

hist(myDataFramet[['colname']], breaks=n)

Super fast for exploratory analysis, not so good for publication.

Person in front of me on the train is paging through nicely structured Excel sheets and I'm fighting the urge to ask whether she's heard the good news about R
#RStats

I have had that problem on mass specs PCs and also long running analysis PCs. There are settings for windows update that will defer updates until a user OKs it. If your IT people will allow you to set it like that!

I might just want to sling funny insults at myself in #rstats 🤔

Oh, Manchester Museum. If you get time go in! It has an amazing Ancient Egypt collection and so much other cool stuff.

This is just the most wonderful data visualization.

This is the way.

I still use 7-zip

Until today I hadn't understood that the control headers in chunks were actually yaml, or that true/false in yaml was case sensitive! So new knowledge!
Also, it turns out quarto-render is forgiving of uppercase in yaml where positron isn't.

Thanks for this.
Can confirm that code chunks with yaml header:
#| eval: false
false, not FALSE, crucially.
Will not be run by the Run All Cells command.

So I'm working with #rstats in #positron writing a #quarto doc. I have a load of code chunks with "eval: FALSE", which are honoured when I render quarto, but are run if I run all chunks from #positron.
How do I stop positron running thos chunks?

Glad to be part of this team calling on global scientific and conservation communities to get on board to protect microbial life, which sustains all forms of life on our planet.

in @natmicrobiol.nature.com

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