I'm truly excited to share the new Nature Methods publication of @msaid

We compare #CHIMERYS against state-of-the-art search engines for DDA/PRM/DIA, and even push into the realm of direct infusion #proteomics

Huge thanks to the other co-first authors and everyone involved #TeamMassSpec

Wanna know how CHIMERYS works?
https://www.nature.com/articles/s41592-025-02663-w
or check out the toot-orial below:

Updates from our continuous development of the #xcms #rstats #metabolomics package:

retention time alignment against external data set
chromatographic peak quality metrics
preformance improvements

All available in current version in @bioconductor release 3.21

Up next: memory-saving analysis of very large data sets!

Time and tide wait for no one. Very pleased to see our more recent 24-hour #PFAS paper featured in LCGC International. Great work by PhD student Nav Singh

https://www.chromatographyonline.com/view/the-effect-of-time-and-tide-on-pfas-concentrations-in-estuaries

Update! The upcoming version of our MsBackendMgf #rstats @bioconductor package will support import from *annotated* MGF files

#MassSpectrometry #TeamMassSpec

https://bit.ly/3FSoTLB

Sharing our Metabonaut resource:

A collection of comprehensive tutorials for LC-MS/MS #metabolomics data analysis in by @phili et al.

Learn raw data processing, annotation & stats with #xcms, #RforMassSpectrometry & @bioconductor - all reproducible & community-driven! #rstats

#CompMS #teammassspec

https://rformassspectrometry.github.io/Metabonaut/

I am super excited to be an invited speaker at AUS-oMicS 2025 in beautiful Cairns. I'll be talking about my work using mass spectrometry to track pollutants in the environment and assess their effects on biological systems via #metabolomics.

The oral abstract submission deadline has been extended until February 14th 2025. Submit yours today and register at https://www.ausomics.com

See you there!

Proud to announce our latest paper: "OpenMS WebApps: Building User-Friendly Solutions for MS Analysis".

We've been working for the last couple of years to provide an interface for people to try out the power of #OpenMS without having to install or download anything. We think the webapp concept works well for this, and with the templates we provide we also think it should be handy for folks wanting to deploy their own locally hosted apps.

Check out the paper here: https://pubs.acs.org/doi/10.1021/acs.jproteome.4c00872

#OpenScience
#opensource
#TeamMassSpec
#Proteomics
#Metabolomics

I initially dismissed compound-specific AA isotope analysis (#CSIA), but not any more, as the more data I see, the less I (evidently) understand metabolic processes. Study of 5 individuals from Franchthi Cave (Greece) challenges assumptions diets doi.org/10.1371/jour... #TeamMassSpec #SciComm

Our proposed hackathon to improve integration of #rstats and #Python packages for #MassSpectrometry was selected for the #EuBIC2025 @EuBIC_MS developer meeting!

Looking forward to expand and improve our SpectryPy package https://bit.ly/4hQfhj1

I always have a sour feeling when I receive google scholar alerts about one of my paper being cited because there are some things I wish I did better. This is about a software, the first I ever published, and it is not great, there are bugs and mistakes. Mostly the result of lack of support. I tried for years to work on a v2 in my free time. But I don’t have a lot of free time, and my mental health and ADHD are in the way.

I am making some very slow progress on my mzML files viewer. But happy about it so far.

Right now the focus is quite narrow. This just about the mzML files themselves not about the spectra. Not yet.

Sometimes I feel like we could QC raw mass spectrometry just by looking at the size of the file… #bioinformatics #teammassspec

More exciting #OpenMS news:
We are proud to announce the release of OpenMS 3.2, now with support for #KNIME 5.3 better export integration with #SIRIUS and improvements to our spectra viewer TOPPView. Read about all the improvements and find a link to download the installers at https://openms.de/news/release3.2/
#OpenScience #TeamMassSpec #opensource

Hi All,
#OpenMS is having our annual user meeting in #Berlin ahead of #HUPO this year October 17-18. For anyone one #TeamMassSpec who is interested in #OpenScience we would love to have you. More information can be found here https://openms.de/news/usermeeting2024/

Does anyone have experience using the Parquet files from ThermoRawFileParser (https://github.com/compomics/ThermoRawFileParser)?

We use the conversion to mzml for everything but when it comes to digging into scan data efficiently I wonder what we could do better. I am also keeping an eye on the MySQL backend for the Spectra package.

Having a great time on the last day of #IMSC2024 some fantastic #teammassspec work on environmental pollution and space geochemistry this morning. Plus a small plug for a great conference next year. #AusOmics

Winding down here in #Melbourne after a great day of #teammassspec #Science at #imsc2024

Props to #ASMS for having more pronoun hangtag options this year.