Matthew Russell
matteomics.bsky.social
Matthew Russell
@matteomics.bsky.social
Measurements want to be accurate;
Experiments want to be elegant;
Data wants to be beautiful and Data wants to be free
#proteomics
#rstats

Reposted by Matthew Russell
Americans make great biologists because we are forged by the hardest challenge in all of biotech: getting flavor from a turkey
November 27, 2025 at 2:35 PM
This post says it very well. I guess transparancy is supposed to enable the quality of work to be better judged after the fact, but agree that may do little to improve quality of the work in the first place.
Transparency about poor inferential practices does not relieve us of the responsibility of not engaging in such practices in the first place. Wish we stopped attributing higher moral value on transparency than doing diligent work and explicitly aiming to minimize the reporting of invalid inferences.
November 26, 2025 at 10:54 PM
Reposted by Matthew Russell
@jameshiggins on UK budget news for what it concerns to #biotech and #diagnostics
November 26, 2025 at 6:40 PM
Reposted by Matthew Russell
that list of four potential peer reviewers you gave your acquisitions editor? one of them is retired, another is chairing their department and simply can't, the third is on leave and has an autoreply up for months, and the fourth replied within 20 seconds to say "no."
November 25, 2025 at 1:46 PM
So much this, I have long wondered why jounals what spesific citations formats. Also, if they do, why not just ask for the doi / pubmed IDs and automate citation formatting to their taste during typsetting.
I have published more than 70 peer reviewed scientific journal articles. I am a reviewer at 50+ journals, and an editor at one journal.

I cannot for the life of me fathom why some journals care so much about reference formatting style. If I can find the paper, you've cited it fine.
a man in a tuxedo is asking why are you booing me i 'm right
ALT: a man in a tuxedo is asking why are you booing me i 'm right
media.tenor.com
November 24, 2025 at 7:31 PM
Reposted by Matthew Russell
And we warned them with our new 2025 State of the Climate Report which you can check out here: doi.org/10.1093/bios...
November 14, 2025 at 7:31 AM
One little bonus of using #git for version control with #quarto for scientific writing is the psycological boost from seeing the git graph fill up as a little progress chart.
November 5, 2025 at 12:10 PM
I had a wonderful run this morning and beautiful walk this afternoon in the north of England. Both of course were curtasy of the ongoing catastraphy of climate change.
EUROPE EXCEPTIONAL NOVEMBER WARMTH

An extraordinary warm spell is affecting all North Africa and Europe,only excluding Italy.
42C in Mauritania, 39 Algeria,>25 in the Balkans (mins up to 19C).

Next days hundreds of records with up to 34C in Turkey.
November 2, 2025 at 5:02 PM
Oh, amzing tool in #Positron with #Quarto for #Rstats scientific publishing. The gitlense extention allows you to compare any pair of previous commits in a single diff view. Am currently rescuing a few ideas lost to an earlier over zelious condensing effort.
October 31, 2025 at 4:39 PM
Amazing Halloween decoration up in #Manchester #UK near the Gay Village. A giant pink spider climbing down wall! The wall belongs to an Alice in Wonderland / Through the Looking Glass themed tea room. I love this city.
October 31, 2025 at 10:28 AM
So I'm working on revisions from co-authors to a paper drafted in #quarto. Co-authors quite reasonably prefer familiarity of word. So I've been trying markitdown (pypi.org/project/mark...) to convert docx back to md and comparing files in notepad++
markitdown
Utility tool for converting various files to Markdown
pypi.org
October 30, 2025 at 4:07 PM
My lucky lucky barber got a lecture on #proteomics and #biomanufacturing this week for this very reason.
Explaining things to people who are learning about them for the first time is the BEST WAY to strengthen your own knowledge and communication skills🤯

You

1) figure out what you don’t know well enough to explain
2) get incredible questions that help you understand what’s not intuitive to newbies
October 24, 2025 at 10:46 AM
A super useful #tidyverse function for #bioinformatics in #rstats with deframe().
Get a named vector of linking protein/gene/kegg identifiers and then attach to a table from elsewhere to translate the new tables ids:
October 23, 2025 at 12:20 PM
This is the way.
This is a good post! I keep using 1234 or 12345, but only for visualization stuff like jittering. For real stuff, I go to random dot org (based on atmospheric noise) and create a random 8+ digit integer, generally one for each brms model I run in a project
We need to have a conversation about random seeds. Don't use 42.
blog.genesmindsmachines.com/p/if-your-ra...
October 22, 2025 at 3:42 PM
Reposted by Matthew Russell
The answers will be given to anyone who follows me, likes ❤️this post, or can wait 48 hours or less.

You will be surprised!
#rstats #dataviz
A "line-up" test has been proposed as a human significance test: Can an observer spot a difference that rejects a null hypothesis?

Here's glyphs for 20 penguins, representing the main variables with visual features.

There are THREE multivariate outliers here. CAN YOU FIND THEM?
October 12, 2025 at 5:50 PM
Reposted by Matthew Russell
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/...
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.
pubs.acs.org
October 10, 2025 at 5:53 PM
Reposted by Matthew Russell
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.
October 9, 2025 at 2:32 PM
Reposted by Matthew Russell
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:
October 8, 2025 at 12:15 PM
I love the science - art interface stuff and @irinabezsonova.bsky.social drawings are really cool.
This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social

Day 2/31
Prompt WEAVE

N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms.

Pdb: 3UA0

Next prompt is CROWN and I would love your suggestions!
October 3, 2025 at 4:58 PM
I just love cutaway images of mass spectrometers, and mini mass spectrometers are always just the cutest.
Dual-Trap “Brick” Miniature Mass Spectrometer with Enhanced Sensitivity and Fragmentation Capabilities #AC pubs.acs.org/doi/10.1021/...
Dual-Trap “Brick” Miniature Mass Spectrometer with Enhanced Sensitivity and Fragmentation Capabilities
Although the miniaturization of mass spectrometry (MS) frequently compromises analytical performance due to size and power limitations, the direct on-site analysis of complex samples requires a miniature mass spectrometer (mini-MS) to have enhanced instrument capabilities. To resolve this challenge, we have developed our “Brick” mini-MS into a next-generation system incorporating a differential-pressure dual-trap configuration. Each trap functions at distinct pressures, enabling parallel and optimized operations: ion accumulation/cooling and dissociation at higher pressures, in conjunction with ion isolation and MS analysis at lower pressure. Efficient ion transfer between the two traps enables parallel ion manipulation and diverse fragmentation modes. The parallel ion accumulation mode boosted the sensitivity of the miniature instrument by ∼20-fold, down to 50 pg/mL. In addition to conventional in-trap collision induced dissociation (CID), transfer dissociation during the ion accelerating and shuttling process and high-pressure collisional dissociation (HpCD) in a higher-pressure trap were also investigated. The results demonstrate that HpCD can generate more extensive ion fragments, which are typically observed in beam-type collisional activation dissociation methods. This study significantly advances the capabilities of mini-MS for high-performance, field-deployable analytical applications.
pubs.acs.org
October 3, 2025 at 9:26 AM
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...
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...
github.com
October 1, 2025 at 10:18 AM
So much this.
I wish more people got this. Science is inefficient. I'd say probably say inherently inefficient. I know we all want to hurry up and make the world a better place with those tax dollars, but I believe the harder we try to rush things, the less effective we will be in the long run.
"Science is not broken, and it most certainly is not dying. It is an inefficient human activity....When we catastrophize, we feed a disillusionment which political actors can weaponize to get rid of scientific evidence they find inconvenient."

#AcademicSky 🧪
September 30, 2025 at 12:04 PM
Reposted by Matthew Russell
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)
September 29, 2025 at 11:50 PM
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.
September 27, 2025 at 3:45 PM