Identification numbers and FDR control of Spectronaut 18 vs DIA-NN 1.9 as benchmarked by Jesper Olsen and colleagues (Nature Methods) www.nature.com/articles/s41...
January 16, 2025 at 6:49 PM
Identification numbers and FDR control of Spectronaut 18 vs DIA-NN 1.9 as benchmarked by Jesper Olsen and colleagues (Nature Methods) www.nature.com/articles/s41...
There is open PTM searching in library free data in SpectroNaut 20! proteomicsnews.blogspot.com/2025/06/spec...
SpectroNaut 20 PTMProbing! Can you finally find PTMs in DIA data?
Check out the above (click to expand) - Yes, that is the bizarre nomenclature used by our friends at SpectroNaut (PG.normal word you'd exp...
proteomicsnews.blogspot.com
June 24, 2025 at 12:10 PM
There is open PTM searching in library free data in SpectroNaut 20! proteomicsnews.blogspot.com/2025/06/spec...
SpectroPipeR—a streamlining post Spectronaut® DIA-MS data analysis R package academic.oup.com/bio...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
February 23, 2025 at 10:40 AM
SpectroPipeR—a streamlining post Spectronaut® DIA-MS data analysis R package academic.oup.com/bio...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
Damn.. #Spectronaut won't even work as a viewer once the license expires.. Damn..
December 2, 2024 at 6:48 PM
Damn.. #Spectronaut won't even work as a viewer once the license expires.. Damn..
Spectronaut 19 played a big role within our single cell analysis pipeline for neutrophils in GBM.
Even with more stringent parameters we could detect > 1,100 and define functional states that are invisible to single cell RNAseq.
Even with more stringent parameters we could detect > 1,100 and define functional states that are invisible to single cell RNAseq.
🚨 New preprint alert!
@pranvera.bsky.social uses single-cell proteomics + #Spectronaut® to decode neutrophil roles in glioblastoma.
1,100 proteins from single cells—revealing dynamic states in brain cancer.
🔬 Read more: www.biorxiv.org/content/10.1...
@pranvera.bsky.social uses single-cell proteomics + #Spectronaut® to decode neutrophil roles in glioblastoma.
1,100 proteins from single cells—revealing dynamic states in brain cancer.
🔬 Read more: www.biorxiv.org/content/10.1...
August 15, 2025 at 10:49 PM
Spectronaut 19 played a big role within our single cell analysis pipeline for neutrophils in GBM.
Even with more stringent parameters we could detect > 1,100 and define functional states that are invisible to single cell RNAseq.
Even with more stringent parameters we could detect > 1,100 and define functional states that are invisible to single cell RNAseq.
News in Proteomics Research blog post | New data analysis strategy in SpectroNaut leverages diagonalPASEF features! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
May 3, 2025 at 7:00 PM
News in Proteomics Research blog post | New data analysis strategy in SpectroNaut leverages diagonalPASEF features! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
Attending #USHUPO2025? Catch our breakfast seminar!☕🥐 We are proud to present @birgitschilling.bsky.social from @buckinstitute.org, alongside Yi-Kai Liu from @purdueuniversity.bsky.social. Don't miss this chance to connect with the experts!
biognosys.com/conferences/...
#Spectronaut #TeamMassSpec
biognosys.com/conferences/...
#Spectronaut #TeamMassSpec
February 12, 2025 at 3:34 PM
Attending #USHUPO2025? Catch our breakfast seminar!☕🥐 We are proud to present @birgitschilling.bsky.social from @buckinstitute.org, alongside Yi-Kai Liu from @purdueuniversity.bsky.social. Don't miss this chance to connect with the experts!
biognosys.com/conferences/...
#Spectronaut #TeamMassSpec
biognosys.com/conferences/...
#Spectronaut #TeamMassSpec
Spectronaut 19 is currently implemented in Proteoscape. It's not a real time analysis, depending on the gradient length, Spectronaut lags 1 or 2 samples behind data aquisition. After running a sequence, multiple samples can be combined in a "second" search. It's convenient. We use it a lot.
November 30, 2024 at 9:16 AM
Spectronaut 19 is currently implemented in Proteoscape. It's not a real time analysis, depending on the gradient length, Spectronaut lags 1 or 2 samples behind data aquisition. After running a sequence, multiple samples can be combined in a "second" search. It's convenient. We use it a lot.
I'm Grateful Tobias Kockmann tested this on the most recent versions of DIA-NN and Spectronaut so I didn't have to :)
July 2, 2025 at 5:34 PM
I'm Grateful Tobias Kockmann tested this on the most recent versions of DIA-NN and Spectronaut so I didn't have to :)
We are happy to announce our latest work as a preprint in proteomics:
Our research showcases significant advancements in DIA on the timsTOF. Through the implementation of diagonal-PASEF and a algorithm in #Spectronaut, we have achieved enhanced peptide identification and precision in human cells.
Our research showcases significant advancements in DIA on the timsTOF. Through the implementation of diagonal-PASEF and a algorithm in #Spectronaut, we have achieved enhanced peptide identification and precision in human cells.
May 2, 2025 at 7:59 AM
We are happy to announce our latest work as a preprint in proteomics:
Our research showcases significant advancements in DIA on the timsTOF. Through the implementation of diagonal-PASEF and a algorithm in #Spectronaut, we have achieved enhanced peptide identification and precision in human cells.
Our research showcases significant advancements in DIA on the timsTOF. Through the implementation of diagonal-PASEF and a algorithm in #Spectronaut, we have achieved enhanced peptide identification and precision in human cells.
SpectroNaut can have false positives similar to match between runs in Maxquant - here is how you improve/fix it - www.biorxiv.org/content/10.1...
Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage redu...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
October 12, 2023 at 10:01 AM
SpectroNaut can have false positives similar to match between runs in Maxquant - here is how you improve/fix it - www.biorxiv.org/content/10.1...
Really looking forward to Spectronaut 20 release at #ASMS2025. We will be showing our new search-engine Kuiper, purpose built for tackling unspecific search spaces.
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
May 30, 2025 at 12:47 PM
Really looking forward to Spectronaut 20 release at #ASMS2025. We will be showing our new search-engine Kuiper, purpose built for tackling unspecific search spaces.
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
It can do an unspecific (peptide length 7-52) open-search in ~30 minutes (2h gradient length Human cell Lysate).
Just a head up, if you did single cell proteomics with the default parameters on Spectronaut 19, your number of IDs are probably inflated by >35%.
This is fixed by having stringent parameters and using versión 20.
This is fixed by having stringent parameters and using versión 20.
September 26, 2025 at 9:01 PM
Just a head up, if you did single cell proteomics with the default parameters on Spectronaut 19, your number of IDs are probably inflated by >35%.
This is fixed by having stringent parameters and using versión 20.
This is fixed by having stringent parameters and using versión 20.
🚀Congrats to Uwe Völker's lab! Their new R package in Bioinformatics enhances #Spectronaut analysis with summary statistics, batch adjustment, peptide-centric analysis, and publication-ready outputs.
📰Publication: academic.oup.com/bioinformati...
#Proteomics #MassSpec
📰Publication: academic.oup.com/bioinformati...
#Proteomics #MassSpec
March 21, 2025 at 12:59 PM
🚀Congrats to Uwe Völker's lab! Their new R package in Bioinformatics enhances #Spectronaut analysis with summary statistics, batch adjustment, peptide-centric analysis, and publication-ready outputs.
📰Publication: academic.oup.com/bioinformati...
#Proteomics #MassSpec
📰Publication: academic.oup.com/bioinformati...
#Proteomics #MassSpec
If you have read www.nature.com/articles/s41... and were concerned about your DIA FDR's with DIA-NN and Spectronaut, this is worth reading. It made me feel a lot better about the most recent versions github.com/Noble-Lab/FD... #proteomics @vadim-demichev.bsky.social @biognosys.bsky.social
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
July 2, 2025 at 5:33 PM
If you have read www.nature.com/articles/s41... and were concerned about your DIA FDR's with DIA-NN and Spectronaut, this is worth reading. It made me feel a lot better about the most recent versions github.com/Noble-Lab/FD... #proteomics @vadim-demichev.bsky.social @biognosys.bsky.social
In Part 2 of our #Spectronaut 20 series, Daniel Green from Greywolf Therapeutics demonstrates how new advances in Spectronaut expand the ERAP1 inhibitor antigen landscape—delivering 47% more peptide discoveries with #directDIA.
Watch the seminar recording: biognosys.com/resources/in...
Watch the seminar recording: biognosys.com/resources/in...
Increasing the identification of ERAP1 inhibitor dependent antigens with Spectronaut 20
In Part 2 of our Spectronaut 20 series, Dan Green (Greywolf Therapeutics) demonstrates how new advances in Spectronaut 20 expand the ERAP1 inhibitor antigen landscape.
biognosys.com
August 27, 2025 at 2:05 PM
In Part 2 of our #Spectronaut 20 series, Daniel Green from Greywolf Therapeutics demonstrates how new advances in Spectronaut expand the ERAP1 inhibitor antigen landscape—delivering 47% more peptide discoveries with #directDIA.
Watch the seminar recording: biognosys.com/resources/in...
Watch the seminar recording: biognosys.com/resources/in...
I'm really liking the new Spectronaut 20 search engine, seems to do a a really good job with unspecific digests. These are examples of chymotrypsin and elastase digests that I searched with no enzyme specificity. Seems to work well!
July 4, 2025 at 12:29 AM
I'm really liking the new Spectronaut 20 search engine, seems to do a a really good job with unspecific digests. These are examples of chymotrypsin and elastase digests that I searched with no enzyme specificity. Seems to work well!
News in Proteomics Research blog post | SpectroNaut 19 has super smart new PTM functionality! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
SpectroNaut 19 has super smart new PTM functionality!
Happy New Year, y'all! Wow, I'm busy with this move, it's 1/7/25?? Typing fast! Okay, so a while back I did a funny thing where I put up ...
proteomicsnews.blogspot.com
January 7, 2025 at 7:40 PM
News in Proteomics Research blog post | SpectroNaut 19 has super smart new PTM functionality! proteomicsnews.blogs...
---
#proteomics #prot-other
---
#proteomics #prot-other
Man it's just not worth keeping older CPU's around. I ran roughly the same set of diaPASEF files in Spectronaut 19.4 and the i9 creamed the 4 year older threadripper. Threadrippers just aren't worth it btw , waste of money
November 20, 2024 at 8:41 PM
Man it's just not worth keeping older CPU's around. I ran roughly the same set of diaPASEF files in Spectronaut 19.4 and the i9 creamed the 4 year older threadripper. Threadrippers just aren't worth it btw , waste of money
🎥 New #Spectronaut Tutorial: Analyzing DIA Data from Isotopically Labeled Samples
In this tutorial, we walk through how to analyze DIA data from labeled workflows, including pulsed SILAC and heavy spike-in peptides.
👉 Watch the tutorial: www.youtube.com/watch?v=bOCP...
#DIAproteomics
In this tutorial, we walk through how to analyze DIA data from labeled workflows, including pulsed SILAC and heavy spike-in peptides.
👉 Watch the tutorial: www.youtube.com/watch?v=bOCP...
#DIAproteomics
February 17, 2026 at 2:33 PM
🎥 New #Spectronaut Tutorial: Analyzing DIA Data from Isotopically Labeled Samples
In this tutorial, we walk through how to analyze DIA data from labeled workflows, including pulsed SILAC and heavy spike-in peptides.
👉 Watch the tutorial: www.youtube.com/watch?v=bOCP...
#DIAproteomics
In this tutorial, we walk through how to analyze DIA data from labeled workflows, including pulsed SILAC and heavy spike-in peptides.
👉 Watch the tutorial: www.youtube.com/watch?v=bOCP...
#DIAproteomics
Nice to see more tutorial videos out there . m.youtube.com/watch?v=_Om1...
Tutorial Series: Everything You Need to Know About Spectronaut®
Introducing our new #Spectronaut video tutorial series!👩🚀📽️In these tutorials, Monika Puchalska, our Software Product Manager, walks you through everythi...
m.youtube.com
January 10, 2024 at 3:01 PM
Nice to see more tutorial videos out there . m.youtube.com/watch?v=_Om1...
⛰️📈 Brixen Proteomics Summer School never disappoints!
A big thank you to everyone who joined our #Spectronaut workshops and brought their insightful questions, energy, and enthusiasm.
See you next time — and until then, let’s keep pushing the boundaries of #proteomics!👋💪
A big thank you to everyone who joined our #Spectronaut workshops and brought their insightful questions, energy, and enthusiasm.
See you next time — and until then, let’s keep pushing the boundaries of #proteomics!👋💪
August 5, 2025 at 12:16 PM
⛰️📈 Brixen Proteomics Summer School never disappoints!
A big thank you to everyone who joined our #Spectronaut workshops and brought their insightful questions, energy, and enthusiasm.
See you next time — and until then, let’s keep pushing the boundaries of #proteomics!👋💪
A big thank you to everyone who joined our #Spectronaut workshops and brought their insightful questions, energy, and enthusiasm.
See you next time — and until then, let’s keep pushing the boundaries of #proteomics!👋💪
Biognosys is proud to sponsor the 15th International Symposium on Proteomics in the Life Sciences hosted by @asbmb.bsky.social! 🎉
Visit our booth to explore our cutting-edge #DIA, #DDA, and targeted software solutions, and learn about our latest #immunopeptidomics work powered by #Spectronaut® 20.
Visit our booth to explore our cutting-edge #DIA, #DDA, and targeted software solutions, and learn about our latest #immunopeptidomics work powered by #Spectronaut® 20.
August 12, 2025 at 2:14 PM
Biognosys is proud to sponsor the 15th International Symposium on Proteomics in the Life Sciences hosted by @asbmb.bsky.social! 🎉
Visit our booth to explore our cutting-edge #DIA, #DDA, and targeted software solutions, and learn about our latest #immunopeptidomics work powered by #Spectronaut® 20.
Visit our booth to explore our cutting-edge #DIA, #DDA, and targeted software solutions, and learn about our latest #immunopeptidomics work powered by #Spectronaut® 20.
Chimerys detected more phosphosites than Spectronaut... Interesting...
November 22, 2023 at 8:08 AM
Chimerys detected more phosphosites than Spectronaut... Interesting...