Michael Marty

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.

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...

New preprint from the lab on IsoDec, our new neural net for isotopic charge state assignment:

chemrxiv.org/engage/chemr...

Does anyone have recommendations for good lab moving companies?

Navigating the Postdoc Experience There are many reasons to consider postdoctoral research after completing a Ph.D. For those interested in academic careers at all levels, a postdoctoral research associate (PDRA) position is often req...

Very excited to share this commentary written by Chae, Daniel, and myself about navigating the postdoc experience. This started out of a discussion in a @femalesinms.bsky.social pod last year. Enjoy!

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

The first @asms.org Winter Conference in Santa Fe is in progress. An intrepid group of skiers and snow boarders took to the slopes at #SkiSantaFe for some free afternoon fun!

#TeamMassSpec

Another major new feature is a complete rewrite of the way we import MS data. If you are looking for Python tools to open Agilent, Waters, or Thermo data, it's a part of the new UniDecImporter.

Check these two new tools out and let me know how it goes! I'm sure there are plenty of bugs to find...

Release UniDec Version 8.0.0 · michaelmarty/UniDec Version 8.0.0 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...

Really excited to release a beta version of UniDec 8.0!

The coolest feature is a new AI-based charge assignment for isotopic resolution data. It's performing a little better than Thrash/Xtract but way faster. Try out IsoDec if you are doing top-down!

github.com/michaelmarty...

Note to self: don’t burn down any buildings in the new place

It’s official! The Marty Lab will be moving to Austin this summer. Looking forward to the new adventure!

Coupling Online Size Exclusion Chromatography with Charge Detection-Mass Spectrometry Using Hadamard Transform Multiplexing Charge detection mass spectrometry (CD-MS) is a powerful technique for the analysis of large, heterogeneous biomolecules. By directly measuring the charge states of individual ions, CD-MS can measure ...

New paper from the group combining separations with CD-MS using Hadamard transform multiplexing: pubs.acs.org/doi/full/10....