Michael Marty

A quick follow up, Firefox seems to work better than all other browsers I’ve tested for some reason

LetA defines a structurally distinct transporter family - Nature The distinct architecture of the Escherichia coli membrane transporter LetA mediates lipid trafficking across the bacterial envelope in partnership with the tunnel-like complex LetB.

Congrats to Christina and the team! Excited to play a small part in this nice story: www.nature.com/articles/s41...

Does anyone else have issues with SciENcv and MyNCBI? It feels like every other click fails. Any tips? I can sometimes get it to work by just clicking the same thing until it does it, but it's rough

I haven’t seen a lot of that, but UMN is doing video applications for that reason. In teaching, I think it’s more about in class assessment now. I do quizzes in class rather than grading homework now

Feeling like it’s been a similar story reading grad school admissions app personal statements

For the 3 of you who are still reading, thanks to everyone who has used UniDec and passed along feedback. I'm grateful for you all!

Also, you'll notice the loss of isotope mode in UniDec. I'm working on merging in IsoDec to create a true mixed-resolution algorithm. But, it's taking longer than I expected to get it. I figured I post this version for the bug fixes. Stay tuned for that later.

I removed Agilent and Sciex data support in this version. The library we use hasn't been actively maintained. We tried to port our own version, but it was causing issues with admin access and getting flagged. Trying to get official support for both, but it's a long legal process. Bummer...

New UniDec release: github.com/michaelmarty...

Lots of bug fixes, improvements, and some under the hood changes to get ready for future features. A few cool new features.

More notes in thread

Pass on congrats from me! How all is well there!

To everyone doing cool data analysis stuff, I'd love to see some analytical chem applicants in this search! Please pass along.

We invite applications for tenured faculty in any area of experimental physical chemistry.
apply.interfolio.com/174607

In this case, we are in a temporary space that we can’t modify. Seems to me like the MS should also have its own breakers in that case. I’ve blown a fuse on the instrument from shorts in boards but I’ve never seen an MS trip a building circuit

Assuming the voltages are correct, has anyone ever had issues running a 15 A mass spectrometer on a 30 A circuit?

GitHub - michaelmarty/MassSpecCodingClub: A community dedicated to education of computer coding applied to mass spectrometry applications. A community dedicated to education of computer coding applied to mass spectrometry applications. - GitHub - michaelmarty/MassSpecCodingClub: A community dedicated to education of computer coding a...

We've got a new MassSpecCodingClub module posted. The videos are linked here: github.com/michaelmarty...

This module teaches how to parse FASTA files and read/write Pandas DataFrames. We explore an application of converting DDA data into an MRM transition list. Enjoy!

This is perfect!

Anyone know of a nitrogen pressure booster that can bring the pressure up from ~90 psi to ~110 psi?

Membrane Proteins: Challenging Biotherapeutic Targets Membrane proteins are about 30% of the human proteome and serve important physiological roles, including chemical transport, cell signaling, and energy transduction. Consequently, they represent abou...

New review article from Hiruni and Farhana on MS of membrane proteins in the context of biotherapeutics: doi.org/10.1002/9781...

(Preprint link here: doi.org/10.26434/che...)

A Fast Neural Network for Isotopic Charge State Assignment Electrospray ionization (ESI) mass spectrometry is an essential technique for chemical analysis in a range of fields. In ESI, analytes can produce multiple charge states, which must be correctly assig...

A Fast Neural Network for Isotopic Charge State Assignment #JACS pubs.acs.org/doi/10.1021/...

A Fast Neural Network for Isotopic Charge State Assignment Electrospray ionization (ESI) mass spectrometry is an essential technique for chemical analysis in a range of fields. In ESI, analytes can produce multiple charge states, which must be correctly assig...

Excited to have this published in @jacs.acspublications.org! IsoDec is a new neural network for charge state assignment with high-resolution MS data. We test it for top-down proteomics. It's free and fast, what else could you want?

pubs.acs.org/doi/full/10....

YouTube video by Michael T Marty IsoDec Tutorial 2: Analyzing LC-MS in the UniDec GUI with TopPIC search

Two new IsoDec tutorial videos to go over top-down proteomics searching with a few different workflows, one with TopPIC and the other with MetaMorpheus @metamorpheus.bsky.social :

youtu.be/OTQbplEezLQ

and

youtu.be/56OZJph48BU

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

Awesome! Send me an email, and I'd be happy to meet up.

YouTube video by Michael T Marty IsoDec Tutorial 1: Analysis of Individual Spectra

Check out the latest tutorial video, from Marty Lab postdoc John Pavek, on how to analyze individual spectra with IsoDec, our new neural network for isotopic deconvolution: youtu.be/aOR37-j28NI

Would anyone be interested in me holding a UniDec/IsoDec office hour at ASMS this year?

Release UniDec Version 8.0.1 · michaelmarty/UniDec Version 8.0.1 UniDec. Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications. Check out a video tutorial: https://www.youtube.com/watch?v=e33...

Well, the USA may be getting worse, but UniDec is getting better. Check out the new version here: github.com/michaelmarty...

Mostly bug fixes. I'd love some people to try it out and let me know how it works on their computers. Hopefully it fixes issues with it getting blocked by antiviruses

Alanine Scanning to Define Membrane Protein–Lipid Interaction Sites Using Native Mass Spectrometry Lipids surrounding membrane proteins interact with different sites on the protein with varying specificities, ranging from highly specific to weak interactions. These interactions can modulate the str...

New paper from the group! Our first with MD simulations included. Congrats to Hiruni and Farhana, who worked really hard on this!

pubs.acs.org/doi/full/10....

If you want to try it out, IsoDec is bundled with UniDec, and there is a simple GUI for doing individual spectra and full files. For doing full top-down proteomics searches, we've bundled it into @metamorpheus.bsky.social, where it really shines!

We ended up with something that worked pretty well, and John Pavek, a postdoc in the group, worked on getting it into a top-down proteomics workflow. It's not leaps and bounds beyond other tools, but it's a decent improvement that nicely balances speed, accuracy, and depth.

For a long time, I've tried to get UniDec to work for isotopic data, but it never really panned out. After getting a grant from NSF to go after the problem, I spent the summer trying to train AI to assign isotopic cluster charge states.