Martin Frejno
@martinfrejno.bsky.social
At MSAID, I am very lucky to work with incredibly intelligent people at the interface between mass spectrometry-based proteomics and artificial intelligence.
Great presentation! Just FYI: It is a little known fact that the MS1 quantification by CHIMERYS on the MSAID Platform works by deconvoluting isotope envelopes in a similar way as JMod since the inception of the platform a year ago. If you are interested in 9-plex DIA support, feel free to reach out!
The talk by Dr. Kevin McDonnell at #SCP2025 is on YouTube:
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains
youtu.be/qgqloCJJa1M?...
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains
youtu.be/qgqloCJJa1M?...
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains, SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 21, 2025 at 9:19 PM
Great presentation! Just FYI: It is a little known fact that the MS1 quantification by CHIMERYS on the MSAID Platform works by deconvoluting isotope envelopes in a similar way as JMod since the inception of the platform a year ago. If you are interested in 9-plex DIA support, feel free to reach out!
Reposted by Martin Frejno
Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.
Assessing error control is fundamental in mass spectrometry-based proteomics. @bo-wen.bsky.social @maccoss.bsky.social @urikeich.bsky.social et al introduce a theoretical foundation for entrapment along with a method for more accurate evaluation of FDR control.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods
A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...
www.nature.com
June 16, 2025 at 6:52 PM
Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.
#TeamMassSpec, don't miss my talk about double dipping in DIA data analysis on Tuesday afternoon at #ASMS2025! It's not as savoury as the one below, but will contain a couple of spicy takes. 🙃
May 31, 2025 at 5:04 PM
#TeamMassSpec, don't miss my talk about double dipping in DIA data analysis on Tuesday afternoon at #ASMS2025! It's not as savoury as the one below, but will contain a couple of spicy takes. 🙃
Reposted by Martin Frejno
Only one week left for #ASMS2025! Join us for our talk on accurate and fast zero-shot peptide spectrum prediction, featuring a deep learning approach that predicts fragment ion intensities—even for peptides with unseen post-translational modifications.
🔗 www.msaid.de/conferences/...
#TeamMassSpec
🔗 www.msaid.de/conferences/...
#TeamMassSpec
May 26, 2025 at 12:57 PM
Only one week left for #ASMS2025! Join us for our talk on accurate and fast zero-shot peptide spectrum prediction, featuring a deep learning approach that predicts fragment ion intensities—even for peptides with unseen post-translational modifications.
🔗 www.msaid.de/conferences/...
#TeamMassSpec
🔗 www.msaid.de/conferences/...
#TeamMassSpec
This is great news for researchers that value data security and privacy when processing proteomics data on-premises and in the cloud! ☁️💻📱
We are excited to announce that MSAID's Information Security Management System (ISMS) was recently certified according to ISO/IEC 27001:2022 by TÜV SÜD! Achieving this milestone highlights our commitment to meet rigorous standards for information security.🔒
#ISO27001 #TÜVSüd #DataSecurity #AI
#ISO27001 #TÜVSüd #DataSecurity #AI
May 15, 2025 at 2:38 PM
This is great news for researchers that value data security and privacy when processing proteomics data on-premises and in the cloud! ☁️💻📱
Reposted by Martin Frejno
CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm that deconvolves any MS2 spectrum, regardless of whether it was acquired by DDA, DIA or PRM, thus unifying analysis of bottom-up proteomics data.
@msaid-de.bsky.social @kusterlab.bsky.social www.nature.com/articles/s41...
@msaid-de.bsky.social @kusterlab.bsky.social www.nature.com/articles/s41...
April 22, 2025 at 5:12 PM
CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm that deconvolves any MS2 spectrum, regardless of whether it was acquired by DDA, DIA or PRM, thus unifying analysis of bottom-up proteomics data.
@msaid-de.bsky.social @kusterlab.bsky.social www.nature.com/articles/s41...
@msaid-de.bsky.social @kusterlab.bsky.social www.nature.com/articles/s41...
So glad to see our paper describing #CHIMERYS finally published in @naturemethods.bsky.social ! Check it out!
🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7
April 22, 2025 at 11:15 AM
So glad to see our paper describing #CHIMERYS finally published in @naturemethods.bsky.social ! Check it out!
Reposted by Martin Frejno
Join us for our upcoming webinar, where we will introduce the latest features of the MSAID Platform, a web-based, fully automated solution for #proteomics data processing, storage, and analysis—powered by CHIMERYS™ 4.
📅 April 1 | 🕒 17:00
🔗 Register here: events.teams.microsoft.com/event/26ff8b...
📅 April 1 | 🕒 17:00
🔗 Register here: events.teams.microsoft.com/event/26ff8b...
March 12, 2025 at 1:26 PM
Join us for our upcoming webinar, where we will introduce the latest features of the MSAID Platform, a web-based, fully automated solution for #proteomics data processing, storage, and analysis—powered by CHIMERYS™ 4.
📅 April 1 | 🕒 17:00
🔗 Register here: events.teams.microsoft.com/event/26ff8b...
📅 April 1 | 🕒 17:00
🔗 Register here: events.teams.microsoft.com/event/26ff8b...
I am happy that our first publication showcasing the MSAID Platform is out! Read all about its unique features or try it for free at platform.msaid.io!
February 25, 2025 at 11:21 AM
I am happy that our first publication showcasing the MSAID Platform is out! Read all about its unique features or try it for free at platform.msaid.io!
Reposted by Martin Frejno
🧪 Join us for a lesson in how to look at your spectra from Sue Weintraub! Using examples from her research, Sue will highlight the importance of looking at mass spectra and teach you how to get started. You won't want to miss it! Register now: ow.ly/P8fw50UrX6m
December 17, 2024 at 10:00 PM
🧪 Join us for a lesson in how to look at your spectra from Sue Weintraub! Using examples from her research, Sue will highlight the importance of looking at mass spectra and teach you how to get started. You won't want to miss it! Register now: ow.ly/P8fw50UrX6m
Reposted by Martin Frejno
I have a radical idea. All DIA tool developers meet in Geneva for a convention and agree to apply certain additional conservative quality filters by default (so yeah, not 10k proteins but “just” 8k…). And then provide users an option to relax the filters at their own risk. Not the other way around.
December 12, 2024 at 1:56 PM
I have a radical idea. All DIA tool developers meet in Geneva for a convention and agree to apply certain additional conservative quality filters by default (so yeah, not 10k proteins but “just” 8k…). And then provide users an option to relax the filters at their own risk. Not the other way around.