#teammassspec — Public Fediverse posts

After a looong journey, I can present you the results of a deep & thorough investigation of human plasma proteolysis by mass spec: SLE N-terminomics paper with a complement C3 fragment(s) is out now in EMBOJ: https://www.embopress.org/doi/full/10.1038/s44318-025-00598-8 - highlights: a nice resource on proteolytically processed N-termini in human plasma of healthy & SLE patients, with a lot of complement bonus for all interested scientists. #SLE #Science #Proteomics #TeamMassSpec #InflammatoryDisease #LupusResearch #C3 #LHF1 1/10

Der Mann hat was neues für #Lupus gefunden - oder wie @kabalak selbst sagen würde:

In conclusion, this study uncovers a new dimension of immune crosstalk: a proteolytic plasma network that generates immunoactive fragments with intrinsic self-regulatory capabilities to modulate #inflammation and tissue injury in complex disease contexts. Deciphering these immunoactivities may pave the way for innovative diagnostic and therapeutic strategies in complement-driven pathologies, potentially benefiting a wide range of inflammatory and autoimmune diseases.

#AutoimmuneDiseases #InflammatoryDisease #Science #SLE #proteomics #MassSpec #TeamMassSpec #LupusResearch

https://www.embopress.org/doi/full/10.1038/s44318-025-00598-8

Happy to announce the publication of our roadmap for #MzPeak, a truely open, performant format for storage of mass spectrometry data:
Please find the paper at https://pubs.acs.org/doi/full/10.1021/acs.jproteome.5c00435

#OpenScience #TeamMassSpec #Proteomics #ProteomicsStandardsInitiative

Happy to announce the publication of our roadmap for #MzPeak, a truely open, performant format for storage of mass spectrometry data:
Please find the paper at https://pubs.acs.org/doi/full/10.1021/acs.jproteome.5c00435

#OpenScience #TeamMassSpec #Proteomics #ProteomicsStandardsInitiative

We just had the kickoff meeting for the #ProteomicsStandardsInitiative #AI working group yesterday. I think it went well, but we'd also like to get more input on what our scope and mandate should be (and as always more volunteers). You can watch the recording here: https://cloud.samwein.com/s/oyjG4ijeEDbiSRF

#OpenScience #TeamMassSpec #Proteomics

We just had the kickoff meeting for the #ProteomicsStandardsInitiative #AI working group yesterday. I think it went well, but we'd also like to get more input on what our scope and mandate should be (and as always more volunteers). You can watch the recording here: https://cloud.samwein.com/s/oyjG4ijeEDbiSRF

#OpenScience #TeamMassSpec #Proteomics

Smart! Stable isotope tracing via LC/MS metabolomics to discover unknown metabolic reactions in cells & mice. 🧪

#teammassspec #metabolomics

https://www.nature.com/articles/s41467-025-60258-7

I love living in the kind of city where this is considered worthy of a plaque. #MassSpec #TeamMassSpec

I love living in the kind of city where this is considered worthy of a plaque. #MassSpec #TeamMassSpec

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:

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 :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!

#TeamMassSpec

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

#water #PFOS #PFOA #estuaries #LCMS #teammassspec #science #ScienceMastodon

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

#water #PFOS #PFOA #estuaries #LCMS #teammassspec #science #ScienceMastodon

Update! The upcoming version of our MsBackendMgf :rstats: #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 :rstats: 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!

#TeamMassSpec #massspectrometry #massspec #ozchem #science #australia

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!

#TeamMassSpec #massspectrometry #massspec #ozchem #science #australia

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

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 :rstats: and #Python :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

#TeamMassSpec #Metabolomics #RforMassSpectrometry

I can’t work on hobby programming projects these days. I am already burned out by work. I hope one day it can be part of my paid work to make better software for peptidomics & co. That would be neat.

#Science #bioinformatics #teammassspec

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.

#Science #bioinformatics #teammassspec

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.

#rust #teammassspec #bioinformatics

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

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

So, we've had feedback on people not being able to attend due to registration costs. We recognize that making science accessible to everyone is important, and so have decided to waive the registration fee for this event (donations to help cover food and bev. would still be appreciated). #TeamMassSpec #HUPO #OpenScience

So, we've had feedback on people not being able to attend due to registration costs. We recognize that making science accessible to everyone is important, and so have decided to waive the registration fee for this event (donations to help cover food and bev. would still be appreciated). #TeamMassSpec #HUPO #OpenScience

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/

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.

#bioinformatics #teammassspec

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.

#bioinformatics #teammassspec

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

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

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.

#TeamMassSpec

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

#TeamMassSpec

Do you work with #MassSpec data? Do you have opinions about #mzML or file formats for storing data in general? The #mzNext group is currently running a survey to identify strengths and weaknesses of current file formats. Please add your voice by filling out the survey here: https://qualtricsxm5l7r46fqr.qualtrics.com/jfe/form/SV_esUoW2IDzZalb6u

#TeamMassSpec #Proteomics #Metabolomics #MassSpectrometry

The more I know about the insides of a ThermoFisher raw file from a mass spectrometer the more I wish I didn't start digging around binary files... #teammassspec

I wrote up the steps needed to analyze a two species, 45 sample (21 rhesus monkey and 24 human), 3 TMTpro plexes, 20-fractions per plex quantitative proteomics experiment. The samples are amniotic fluid at multiple gestational ages. The blog post is at: https://github.com/pwilmart/Human_rhesus_TMT.

#TeamMassSpec
#Proteomics
#teamProteomics

#IMSC2024 has a competition running this week giving away free student registrations. Unfortunately you will have to visit LinkedIn, Instagram or the bad place to enter!

You can sign up for conference updates at www.imsc2024melbourne.com

#TeamMassSpec #massspectrometry #massspec #proteomics #lipidomics #metabolomics #chemistry

RT @BePa_Proteomics: Join the ECR event and get a chance to win a travel grant! Registration is open!@EuPAProteomics #TeamMassSpec #proteomics

RT @byu_sam: #TeamMassSpec. question about tools for TMT quant. Which tools incorporate the MS1 intensity into the quantitation from MS2-based reporter ions?
I know that @nesvilab does this with Fragger. But does anyone else?

RT @byu_sam: #TeamMassSpec. question about tools for TMT quant. Which tools incorporate the MS1 intensity into the quantitation from MS2-based reporter ions?
I know that @nesvilab does this with Fragger. But does anyone else?

RT @FemalesInMS: We are very excited that our FeMS “Out of the Shadows” Cohort 2 leadership training kicks off tomorrow in Munich with our partner @BrukerMassSpec! We had a great networking evening and can't wait for tomorrow's program #TeamMassSpec #Leadership @DART_MS

RT @DrLauraD22: Calling all #TeamMassSpec students interested in #proteomics. We have some excellent #PhD opportunities ⁦@WEHI_research⁩ proteomics facility. Please share! ⁦@FemalesInMS⁩ ⁦@PMV_Australia⁩ ⁦@LorneProteomics⁩ ⁦@hupo_org⁩

Happy to announce that we've just put up our preprint for the #OpenMS 3.0 release:

https://www.researchsquare.com/article/rs-3286368/v1

OpenMS is the by far the largest software project that I've ever worked on, and this is the first major release during my tenure here. Happy to answer any questions.

#TeamMassSpec #FOSS #OpenScience #OpenSource #Proteomics #massSpectrometry

RT @byu_sam: After reading this, I am struck that all the negative examples (where CV is wonky) are because of terrible data quality, like letting in peptides with no FDR filter.

But is CV a bad metric if I am doing proper FDR filtering? #TeamMassSpec

RT @: Assuming spray voltage is fine, what is the cause of the retrograde movement of the mobile along the emitter during ESI? #TeamMassSpec #Protoemics