Anneliese
@aphettochemist.bsky.social
Proteomics | mass spec | scientific illustration | Magic: the Gathering
Reposted by Anneliese
October 5, 2025 at 8:10 AM
Reposted by Anneliese
With 𝗗𝗜𝗔-𝗡𝗡 𝟮.𝟯.𝟬 Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: github.com/vdemichev/Di...
September 26, 2025 at 9:52 AM
With 𝗗𝗜𝗔-𝗡𝗡 𝟮.𝟯.𝟬 Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: github.com/vdemichev/Di...
Reposted by Anneliese
In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
August 17, 2025 at 9:20 AM
In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
Reposted by Anneliese
PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...
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#proteomics #prot-paper
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#proteomics #prot-paper
July 17, 2025 at 2:40 PM
PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...
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#proteomics #prot-paper
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#proteomics #prot-paper
Reposted by Anneliese
Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social !
www.biorxiv.org/content/10.1...
This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.
1/?
www.biorxiv.org/content/10.1...
This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.
1/?
Native, Spatiotemporal Profiling of the Global Human Regulome
The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...
www.biorxiv.org
July 2, 2025 at 3:08 PM
Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social !
www.biorxiv.org/content/10.1...
This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.
1/?
www.biorxiv.org/content/10.1...
This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.
1/?
Reposted by Anneliese
‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
www.verwaltung.uni-halle.de
June 25, 2025 at 12:44 PM
‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
Reposted by Anneliese
Error control in proteomics mass spectrometry analysis is hard. We came up with a way to evaluate error control. Upshot: for old-school DDA data, not so bad. For DIA data, no existing tool successfully controls the false discovery rate!
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 8:57 PM
Error control in proteomics mass spectrometry analysis is hard. We came up with a way to evaluate error control. Upshot: for old-school DDA data, not so bad. For DIA data, no existing tool successfully controls the false discovery rate!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Favorite piece of vendor swag from ASMS.
June 12, 2025 at 5:10 PM
Favorite piece of vendor swag from ASMS.
Starting to work on something 👀
June 8, 2025 at 2:02 AM
Starting to work on something 👀
Reposted by Anneliese
DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...
May 30, 2025 at 8:36 AM
DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...
Reposted by Anneliese
📢 Save the date!
The applications for the Empowerment Award for Q3 2025 will open soon 🏆
You can find more information here ➡️ femalesinms.com/empowerment/
The applications for the Empowerment Award for Q3 2025 will open soon 🏆
You can find more information here ➡️ femalesinms.com/empowerment/
May 2, 2025 at 5:12 PM
📢 Save the date!
The applications for the Empowerment Award for Q3 2025 will open soon 🏆
You can find more information here ➡️ femalesinms.com/empowerment/
The applications for the Empowerment Award for Q3 2025 will open soon 🏆
You can find more information here ➡️ femalesinms.com/empowerment/
New photo-crosslinker just dropped 👀
Heterobifunctional by warhead, K-K reactive, and partially tris tolerant.
I believe that this could be made into a cleavable version by reducing compound 1b to a primary amine and reacting with DSC to make an NHS-carbamate instead of an NHS-ester. Great work.
Heterobifunctional by warhead, K-K reactive, and partially tris tolerant.
I believe that this could be made into a cleavable version by reducing compound 1b to a primary amine and reacting with DSC to make an NHS-carbamate instead of an NHS-ester. Great work.
Delighted to share our latest preprint on the design of photoactivatable and lysine reactive oNBA-based reagents for chemical crosslinking-mass spectrometry. We think that these new tools will enable a range of novel structural proteomics applications! www.biorxiv.org/content/10.1...
Design and Characterisation of Photoactivatable and Lysine Reactive o-Nitrobenzyl Alcohol-Based Crosslinkers
Photoreactive groups are invaluable tools in structural proteomics, offering reagent-free activation and temporal control of protein labelling. However, traditional UV-activatable functional groups of...
www.biorxiv.org
May 10, 2025 at 2:08 PM
New photo-crosslinker just dropped 👀
Heterobifunctional by warhead, K-K reactive, and partially tris tolerant.
I believe that this could be made into a cleavable version by reducing compound 1b to a primary amine and reacting with DSC to make an NHS-carbamate instead of an NHS-ester. Great work.
Heterobifunctional by warhead, K-K reactive, and partially tris tolerant.
I believe that this could be made into a cleavable version by reducing compound 1b to a primary amine and reacting with DSC to make an NHS-carbamate instead of an NHS-ester. Great work.
Reposted by Anneliese
✈️ ASMS 2025 Early Career Researcher Travel Awards ✈️
📢 Call for Applications 📢
Don’t miss this opportunity!
Applications are open from *May 12th to 23rd* 📧
hispanicsandlatinxinms.org/asms-2025-ea...
#ASMS2025 #MSCommunity
📢 Call for Applications 📢
Don’t miss this opportunity!
Applications are open from *May 12th to 23rd* 📧
hispanicsandlatinxinms.org/asms-2025-ea...
#ASMS2025 #MSCommunity
May 9, 2025 at 6:50 PM
✈️ ASMS 2025 Early Career Researcher Travel Awards ✈️
📢 Call for Applications 📢
Don’t miss this opportunity!
Applications are open from *May 12th to 23rd* 📧
hispanicsandlatinxinms.org/asms-2025-ea...
#ASMS2025 #MSCommunity
📢 Call for Applications 📢
Don’t miss this opportunity!
Applications are open from *May 12th to 23rd* 📧
hispanicsandlatinxinms.org/asms-2025-ea...
#ASMS2025 #MSCommunity
Reposted by Anneliese
Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!
May 5, 2025 at 4:06 AM
Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!
This is a really nice application of XLMS to look at viral-host protein interaction. Impressive work from Fan Liu, giving me lots of ideas.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Snapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infection
Influenza A virus (IAV) exploits the host cellular machinery to facilitate its replication, yet many host-IAV interactions remain unexplored in the cellular context. Detailed information about interac...
www.biorxiv.org
March 30, 2025 at 12:21 PM
This is a really nice application of XLMS to look at viral-host protein interaction. Impressive work from Fan Liu, giving me lots of ideas.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Anneliese
🧪 I was a postdoc at NIH 25 years ago. Without this experience I would not have been able to understand the beauty and power of science. I am now telling my students how important it is to stand up for science. 🧪 Otherwise ignorance will win.
@standupforscience.bsky.social
#supportscience
#saveNIH
@standupforscience.bsky.social
#supportscience
#saveNIH
March 16, 2025 at 9:41 AM
🧪 I was a postdoc at NIH 25 years ago. Without this experience I would not have been able to understand the beauty and power of science. I am now telling my students how important it is to stand up for science. 🧪 Otherwise ignorance will win.
@standupforscience.bsky.social
#supportscience
#saveNIH
@standupforscience.bsky.social
#supportscience
#saveNIH
City Hall, Philly.
Thinking of all of the NIH scientists right now.
Thinking of all of the NIH scientists right now.
March 7, 2025 at 10:12 PM
City Hall, Philly.
Thinking of all of the NIH scientists right now.
Thinking of all of the NIH scientists right now.
Found out that BLAST is down while working on a project that I need it for. Absolutely bonkers that critical bioinformatics tools are being slashed.
March 1, 2025 at 11:38 PM
Found out that BLAST is down while working on a project that I need it for. Absolutely bonkers that critical bioinformatics tools are being slashed.
A great first day
February 24, 2025 at 3:15 AM
A great first day
Rooting around in ProteomeXchange today, and developing a deep desperation for people to name their rawfiles clearly.
February 14, 2025 at 9:19 PM
Rooting around in ProteomeXchange today, and developing a deep desperation for people to name their rawfiles clearly.
Fried my old motherboard last week but have now upgraded enough to do proteomics at home 👀
February 1, 2025 at 1:27 PM
Fried my old motherboard last week but have now upgraded enough to do proteomics at home 👀
Reposted by Anneliese
DIA-NN 2.0 release is almost ready, will come with some big news. One is scanning methods support, at the moment doing some tuning of the algorithm using Synchro-PASEF data :) Turns out, 'Q1 information' is really helpful for gaining peptidoform confidence. Likely also channel-confidence in plexDIA.
January 9, 2025 at 12:16 PM
DIA-NN 2.0 release is almost ready, will come with some big news. One is scanning methods support, at the moment doing some tuning of the algorithm using Synchro-PASEF data :) Turns out, 'Q1 information' is really helpful for gaining peptidoform confidence. Likely also channel-confidence in plexDIA.