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
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
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
Props to #ASMS for having more pronoun hangtag options this year.
Two of our workshops/tutorials are now also on #zenodo and have a DOI
- Mass spectrometry data analysis with Spectra: https://doi.org/10.5281/zenodo.11210190
- Exploring and analyzing LC-MS data with xcms and Spectra: https://doi.org/10.5281/zenodo.11185521
Both are based on current @bioconductor release 3.19 and provide 
docker containers including all data and packages for reproducibility.
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
Is anyone using a self-hosted Zotero server? Is it possible?
The few projects I found are no longer maintained. And my impression from questions on the Zotero github issues is that this is not their priority at all.
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
Hey #TeamMassSpec, I'm having issues with a contaminant ion @ 248.9 m/z in -ve ion mode when running 90% ACN 10 mM AmOAc at pH 9. Found a thread on research gate suggesting it comes from the ACN but have tried two brands now with no joy. Has anyone else had this problem?
Research gate link: https://researchgate.net/post/What-is-this-contaminant-with-m-z-2489718
ACN brands tried: Fisher Sci Optima, Supelco LiChroSolv. LiChroSolv has a lot less of it than Fisher Sci.
RT @: Always good to see new #massspec tools available.Dear #proteomicscommunity and #TeamMassSpec, I am happy to share HowDirty, an R package that facilitates evaluating and reporting molecular contaminants in LC-MS experiments.
https://authorea.com/users/643346/articles/656759-howdirty-an-r-package-to-evaluate-molecular-contaminants-in-lc-ms-experiments…
#teammassspec @massspec you can probably guess what her father is working with?
(Thanks to the whole @warscheidlab for this great birth gift for our daughter!)
@academicchatter
What's the job market in the USA for proteomics / bioinformaticians people? Is there a huge supply of people trained analysing mass spec data and doing bioinformatics or do you have to train bioinformaticians into proteomics?
#PhDposition 
@warscheidlab
️ Come and join our all-new lab at #uniwuerzburg
for studying #StressSignaling by #proteomics, become a part of the great #TeamMassSpec and start your #PhDlife now. #vacancy
@massspec Details:
https://www.findaphd.com/phds/project/phd-position-f-m-d-in-signaling-proteomics-and-proteostasis/?p156531
@drupad
There are a bunch of folks who moved over in November. Not sure how many are still active.
I’ve checked the feature request and a non-chronologically sorted home timeline is a contentious topic (not quite as heated as quote re-posting). I would definitely like it as an option since the more follows I have (and the more active they are), the more content I may need to quickly skim. Feature not a bug, but maybe an optional bug I can toggle on and off?
What is the positive control for a given data #normalization strategy?
To measure if strategy x worked, if its not badly or overtly done?
#metabolomics #proteomics #massspec #teammassspec hive mind?
A great resource to get started with building your #Mastodon network #twittermigration
https://github.com/nathanlesage/academics-on-mastodon
PS: I've added a PR to get #teamMassSpec on that list.
#teammassspec Serious problem here. Some of you folks like to convert your vendor files to mzML for storage in pride/massive. Please don't. Once your fry an egg you can't unfry it. Some of your mzML converters are BROKEN! You're not doing us favors. If you want to provide both vendor and mzML that kudos.
Convince me I'm wrong.
about 1/10th of the people I follow on twitter I've also found on mastodon. Not a bad start overall 
much higher percentage from #teamMassSpec than from the #immunology side though
