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#massspectrometry

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Public
Amelia Cervera 🧬

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment.
#Microproteins #sORFs #MassSpectrometry #Proteomics #Preprint
biorxiv.org/content/10.1101/20

bioRxiv · Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessmentThousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist. ### Competing Interest Statement J.R.P. has received research honoraria from Novartis Biosciences and is a paid consultant for ProFound Therapeutics. P.V.B. is a cofounder and shareholder of EIRNA Bio. T.F.M. is a consultant for and holds equity in Velia Therapeutics. A.-R.C. is a member of the scientific advisory board for Flagship Labs 69, Inc (ProFound Therapeutics).
Public
Nina Davtian

Let me explain in the following #thread why the (auto-)citation of Davtian et al. (2018) Organic Geochemistry—my second first-authored #PhD #scientific #publication—by De Jonge et al. (2024) Geochemistry, Geophysics, Geosystems matters to me and my current CEREGE colleagues at CEREGE
doi.org/10.1016/j.orggeochem.2 👇🏻 (1/9)
#Science
#ScienceMastodon #AcademicMastodon
#Paper
#GDGTs #isoGDGTs #brGDGTs
#Index #Indices #ClimateProxies
#LiquidChromatography #MassSpectrometry
mastodon.world/@nina_davtian/1

Public
Nina Davtian

I am so glad to be one of the two ICTA-UAB representants—the other is Joan Villanueva—for the interlaboratory #study led by Cindy De Jonge and Francien Peterse!
doi.org/10.1029/2024GC011583
Let's summarize this important #scientific #publication with the following #thread! 👇🏻 (1/6)
#Science
#ScienceMastodon #AcademicMastodon
#WomenInSTEM
#Paper #OpenAccess #OpenAccessWeek #OpenAccessWeek24 #OpenAccessWeek2024
#RoundRobin #Reproducibility
#LiquidChromatography #MassSpectrometry
#GDGTs #brGDGTs

Header of the online article by De Jonge et al. (2024) GGG (https://doi.org/10.1029/2024GC011583) entitled "Interlaboratory Comparison of Branched GDGT Temperature and pH Proxies Using Soils and Lipid Extracts" and published as a gold open access paper in the AGU journal Geochemistry, Geophysics, Geosystems. The author list is organized as follows: the first two authors (Cindy De Jonge and Francien Peterse) led the study and contributed equally to the paper, with the help of the third and fourth authors (Klaas G. J. Nierop and Thomas M. Blattmann), whereas the rest of the authors (including me, Nina Davtian) are (mostly) ordered alphabetically as representants of the participating laboratories. Screenshot taken by Nina Davtian (that's me!).
Public
Nina Davtian

My first first-authored #scientific #publication as a former #postdoc at ICTA-UAB, published in #Journal of #Chromatography A one year and a half ago, deserves a #thread on #Mastodon as well!
We selectively extract #levoglucosan and its isomers from complex matrices, such as #sediments, for quantification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS)!
#Science #ScienceMastodon #Paper
#LiquidChromatography #MassSpectrometry
doi.org/10.1016/j.chroma.2023. (1/28)

Public
Laurent Gatto

The startup message of the #MSnbase package for #MassSpectrometry and #Proteomics has been update in version 2.29.2, and now officially asks users to look into the #RforMassSpectrometry initiative packages:

> library(MSnbase)
This is MSnbase version 2.29.2
Visit lgatto.github.io/MSnbase/ to get started.
Consider switching to the 'R for Mass Spectrometry'
packages - see RforMassSpectrometry.org for details.

lgatto.github.ioBase Functions and Classes for Mass Spectrometry and ProteomicsMSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Public
Dr. Samuel Wein

Life is funny sometimes. In the fall of 2021 I ended up chatting with my neighbor on a flight from Frankfurt to Philly. He asks what I do for work. I said that I wrote software for the analysis of #RNA modifications by #massSpectrometry. He seemed impressed, and asked if I was familiar with the work of Katalin #Karikó. I told him "of course". He very proudly responded "I'm her husband" and pulled out a photo of them together with their daughter and the king of Spain. 1/x
#mRNA #NobelPrize

Public
Dr. Samuel Wein

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

researchsquare.com/article/rs-

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.

www.researchsquare.comOpenMS 3 expands the frontiers of open-source computational mass spectrometryMass spectrometry has become an indispensable tool in the life sciences. The new major version 3 of the computational framework OpenMS provides significant advancements regarding open, scalable, and reproducible high-throughput workflows for proteomics, metabolomics, and oligonucleotide mass spec...
#TeamMassSpec#FOSS#OpenScience
Public *
Dr. Sarah Fantin

( hoping a late #introduction is better than none
at all! )

Hi everyone,

I'm Sarah, a #chemistry prof at Hanover College in Indiana. My PhD work was in #membrane #protein #massspectrometry and now I've got a special interest in anything #neuro related! I teach an entire course on the biochemistry of psychoactive drugs and I'm still trying to get into research in that field because its super interesting to me! In the mean time I'm doing some #lcms of #cannabinoids and focusing on teaching.

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