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Michael Marty @michaelmarty.bsky.social · 14d

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

Michael Marty @michaelmarty.bsky.social · 15d

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

The University of Texas at Austin Department of Chemistry @utaustinchemistry.bsky.social · 15d

We invite applications for tenure-track faculty whose research programs broadly align with the themes of Artificial Intelligence and Data Analytics (AI+DA) in the areas of life sciences, bioorganic, synthesis, analytical, materials, and generative AI.
apply.interfolio.com/174602

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Reposted by Michael Marty

The University of Texas at Austin Department of Chemistry @utaustinchemistry.bsky.social · 15d

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

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Michael Marty @michaelmarty.bsky.social · Aug 11

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

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Michael Marty @michaelmarty.bsky.social · Aug 6

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

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Michael Marty @michaelmarty.bsky.social · Jul 18

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!

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...

github.com

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Michael Marty @michaelmarty.bsky.social · Jun 30

This is perfect!

Michael Marty @michaelmarty.bsky.social · Jun 27

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

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Michael Marty @michaelmarty.bsky.social · Jun 12

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...)

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...

doi.org

Reposted by Michael Marty

BioMassSpec @realbiomassspec.bsky.social · Jun 10

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...

pubs.acs.org

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Michael Marty @michaelmarty.bsky.social · Jun 10

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....

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...

pubs.acs.org

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Michael Marty @michaelmarty.bsky.social · May 14

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

IsoDec Tutorial 2: Analyzing LC-MS in the UniDec GUI with TopPIC search

YouTube video by Michael T Marty

youtu.be

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Reposted by Michael Marty

Mingxun Wang @mingxunwang.bsky.social · May 12

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.

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Michael Marty @michaelmarty.bsky.social · May 1

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

Michael Marty @michaelmarty.bsky.social · May 1

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

IsoDec Tutorial 1: Analysis of Individual Spectra

YouTube video by Michael T Marty

youtu.be

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Michael Marty @michaelmarty.bsky.social · Mar 24

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

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Michael Marty @michaelmarty.bsky.social · Mar 15

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

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...

github.com

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Michael Marty @michaelmarty.bsky.social · Mar 6

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....

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...

pubs.acs.org

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Michael Marty @michaelmarty.bsky.social · Feb 21

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!

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Michael Marty @michaelmarty.bsky.social · Feb 21

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.

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Michael Marty @michaelmarty.bsky.social · Feb 21

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.

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Michael Marty @michaelmarty.bsky.social · Feb 21

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

chemrxiv.org/engage/chemr...

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...

chemrxiv.org

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Michael Marty @michaelmarty.bsky.social · Feb 21

Does anyone have recommendations for good lab moving companies?

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Michael Marty @michaelmarty.bsky.social · Feb 20

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/...

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...

pubs.acs.org

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Reposted by Michael Marty

ASMS @asms.org · Jan 26

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

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