Hirak Das
@hirakdas.bsky.social
Marie Curie ESR at Warscheid Lab, University of Würzburg | Mass Spectrometry | Spatial Proteomics and multi-omics | Peroxisomes | Loves playing with MS, Big Data, and AI
Great work by @dwendscheck.bsky.social from our lab and everyone else involved! This is a collaborative effort from many labs, which led to the identification and characterization a new (and important) Peroxin in more than 20 years!!
👏 Well deserved!
👏 Well deserved!
Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics
#Biochemistry: #PEX39, a newly discovered #peroxin protein, transports enzymes into #peroxisomes like a relay racer. New paper @natcellbio.nature.com – congratulations to @dwendscheck.bsky.social @warscheidlab.bsky.social et al!
➡️ www.uni-wuerzburg.de/en/news-and-...
➡️ www.uni-wuerzburg.de/en/news-and-...
August 5, 2025 at 5:42 PM
Great work by @dwendscheck.bsky.social from our lab and everyone else involved! This is a collaborative effort from many labs, which led to the identification and characterization a new (and important) Peroxin in more than 20 years!!
👏 Well deserved!
👏 Well deserved!
Happy to share our recent publication where we present the most up to date membrane protein inventory of #Glycosomes and identified the long sought trypanosomal PEX15.
Thanks to everyone involved for this amazing collaborative effort to combine #proteomics with #functional #analysis.
Thanks to everyone involved for this amazing collaborative effort to combine #proteomics with #functional #analysis.
High-confidence glycosomal membrane protein inventory unveils trypanosomal peroxin PEX15 #CellRep #MassSpec www.cell.com/cell-reports...
High-confidence glycosomal membrane protein inventory unveils trypanosomal peroxin PEX15
Trypanosoma and Leishmania infections cause devastating neglected tropical diseases.
These parasites harbor peroxisome-related organelles called glycosomes, which are
essential for their survival. Kri...
www.cell.com
April 28, 2025 at 2:21 PM
Happy to share our recent publication where we present the most up to date membrane protein inventory of #Glycosomes and identified the long sought trypanosomal PEX15.
Thanks to everyone involved for this amazing collaborative effort to combine #proteomics with #functional #analysis.
Thanks to everyone involved for this amazing collaborative effort to combine #proteomics with #functional #analysis.
Reposted by Hirak Das
Be courageous to be creative.
Making substantive progress in proteomics benefits from:
1️⃣ Appreciating the fundamental differences in scale and complexity between proteomics & transcriptomics
2️⃣ Recognizing the challenges without being intimidated. Being courageous to be creative.
blog.slavovlab.net/2023/09/23/t...
1️⃣ Appreciating the fundamental differences in scale and complexity between proteomics & transcriptomics
2️⃣ Recognizing the challenges without being intimidated. Being courageous to be creative.
blog.slavovlab.net/2023/09/23/t...
March 25, 2025 at 1:30 PM
Be courageous to be creative.
Reposted by Hirak Das
One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...
March 4, 2025 at 9:09 AM
One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...
Reposted by Hirak Das
Please don’t stop sharing and posting your science because of the current attack on it, it is still valuable and reminds us what the fight is for
February 17, 2025 at 11:50 PM
Please don’t stop sharing and posting your science because of the current attack on it, it is still valuable and reminds us what the fight is for
Had a great time keeping up with the "state-of-the-art" #Thermo #Astral MS instrument and analysis! 👍 Thanks to Michal!
We go deeper into the #proteome, faster than ever!!
Exciting times ahead.. ☀️
We go deeper into the #proteome, faster than ever!!
Exciting times ahead.. ☀️
Happy @warscheidlab.bsky.social Team after three days training on the Thermo #Astral. Many thanks to Michal Nadler Holly for such a great course! #TeamMassSpec #proteomics #PhDlife @lakshitaaa.bsky.social @johannes-uni-wue.bsky.social @hirakdas.bsky.social
February 14, 2025 at 4:04 PM
Reposted by Hirak Das
In 2021, we introduced plexDIA: plexdia.slavovlab.net
It enabled many studies, but suitable tags have remained a limitation.
Soon, @parallelsq.bsky.social will introduce tags that improve multiplexing, sensitivity & coverage, helping realize huge potential pubs.acs.org/doi/10.1021/...
Stay tuned!
It enabled many studies, but suitable tags have remained a limitation.
Soon, @parallelsq.bsky.social will introduce tags that improve multiplexing, sensitivity & coverage, helping realize huge potential pubs.acs.org/doi/10.1021/...
Stay tuned!
Home
Sensitive, accurate and high-throughput proteomics by multiplexed data-independent acquisition (plexDIA). plexDIA for increasing proteomics throughput Slavov Laboratory and single-cell proteomics cent...
plexdia.slavovlab.net
February 12, 2025 at 2:04 PM
In 2021, we introduced plexDIA: plexdia.slavovlab.net
It enabled many studies, but suitable tags have remained a limitation.
Soon, @parallelsq.bsky.social will introduce tags that improve multiplexing, sensitivity & coverage, helping realize huge potential pubs.acs.org/doi/10.1021/...
Stay tuned!
It enabled many studies, but suitable tags have remained a limitation.
Soon, @parallelsq.bsky.social will introduce tags that improve multiplexing, sensitivity & coverage, helping realize huge potential pubs.acs.org/doi/10.1021/...
Stay tuned!
Reposted by Hirak Das
Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects.
📄 nature.com/articles/s41...
🌐 search.foldseek.com
📄 nature.com/articles/s41...
🌐 search.foldseek.com
February 6, 2025 at 8:25 AM
Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects.
📄 nature.com/articles/s41...
🌐 search.foldseek.com
📄 nature.com/articles/s41...
🌐 search.foldseek.com
Reposted by Hirak Das
Scientists have created an actual treatment for prions, the cause of Creutzfeldt–Jakob disease in humans, chronic wasting disease in deer, & mad cow disease.
"Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor". #ShareGoodNewsToo
"Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor". #ShareGoodNewsToo
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts...
www.science.org
February 3, 2025 at 3:55 PM
Scientists have created an actual treatment for prions, the cause of Creutzfeldt–Jakob disease in humans, chronic wasting disease in deer, & mad cow disease.
"Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor". #ShareGoodNewsToo
"Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor". #ShareGoodNewsToo
Reposted by Hirak Das
The good idea comes when one person feels comfortable enough to say something that might make them look stupid and their friend is open enough to recognize its potential.
December 8, 2024 at 4:23 AM
The good idea comes when one person feels comfortable enough to say something that might make them look stupid and their friend is open enough to recognize its potential.
Reposted by Hirak Das
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
www.nature.com
December 6, 2024 at 8:52 PM
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...
Reposted by Hirak Das
After long-time review, #nanoSPLITS is finally published. I am deeply grateful to my colleagues who made this work possible, especially @cajunscience.bsky.social. I am also grateful to the support of our single-cell proteomics community during the peer review on Nature Communication!
Now this is a paper I had long been waiting for! NanoSPLITS is out! Parallel single cell proteomic and transcriptomic measurements from the same cell! Great work from @cajunscience.bsky.social and @nanopots.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting - Nature Communications
Single-cell multiomics can provide broad insights into gene/protein regulatory networks and cellular diversity. Here, authors develop nanoSPLITS, a nanodroplet splitting approach for global profiling ...
www.nature.com
December 6, 2024 at 12:41 AM
After long-time review, #nanoSPLITS is finally published. I am deeply grateful to my colleagues who made this work possible, especially @cajunscience.bsky.social. I am also grateful to the support of our single-cell proteomics community during the peer review on Nature Communication!
Very important point raised by @rongfan8.bsky.social here:
www.nature.com/articles/s41...
I think we are slowly getting there. At least one step at a time, thanks to technological feats gained in MS community. For e.g recent nanoSPLITS method by @nanopots.bsky.social
The future is exciting!
www.nature.com/articles/s41...
I think we are slowly getting there. At least one step at a time, thanks to technological feats gained in MS community. For e.g recent nanoSPLITS method by @nanopots.bsky.social
The future is exciting!
Integrative spatial protein profiling with multi-omics - Nature Methods
Spatial proteomics holds the potential to transform the study of proteins in situ in complex tissues, but it needs to be integrated with other layers of omics data to gain a holistic view of cellular ...
www.nature.com
December 6, 2024 at 7:50 PM
Very important point raised by @rongfan8.bsky.social here:
www.nature.com/articles/s41...
I think we are slowly getting there. At least one step at a time, thanks to technological feats gained in MS community. For e.g recent nanoSPLITS method by @nanopots.bsky.social
The future is exciting!
www.nature.com/articles/s41...
I think we are slowly getting there. At least one step at a time, thanks to technological feats gained in MS community. For e.g recent nanoSPLITS method by @nanopots.bsky.social
The future is exciting!
Reposted by Hirak Das
Scared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance
Can processes occurring in one individuals nervous system influence the physiology of the descendants? Here we explored the provocative hypothesis that parents sensation or perception of environmental...
www.biorxiv.org
December 5, 2024 at 7:32 PM
Scared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Hirak Das
Could one envision a synthetic receptor technology that is fully programmable, able to detect diverse extracellular antigens – both soluble and cell-attached – and convert that recognition into a wide range of intracellular responses, from gene expression and real-time fluorescence to modulation..
December 4, 2024 at 4:05 PM
Could one envision a synthetic receptor technology that is fully programmable, able to detect diverse extracellular antigens – both soluble and cell-attached – and convert that recognition into a wide range of intracellular responses, from gene expression and real-time fluorescence to modulation..
Reposted by Hirak Das
Great to see, that @altmetric.com is now also tracking and reporting on activity on @bsky.app. This is a great further step to make bluesky the key social media network for science. (1/2) www.altmetric.com/de...
Report for: Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050
In the top 5% of all research outputs scored by Altmetric
www.altmetric.com
December 3, 2024 at 5:45 AM
Great to see, that @altmetric.com is now also tracking and reporting on activity on @bsky.app. This is a great further step to make bluesky the key social media network for science. (1/2) www.altmetric.com/de...
Reposted by Hirak Das
Related - there are whole high profile “protein atlases” based on transcript expression that are clearly inaccurate - proteomicsnews.blogspot.com/2024/06/re-r...
Re-revisited the organ specific protein aging study - "organ specificity" is not supported by protein level data!
For anyone unfortunate to visit this blog in the past, you might have seen some of my early analysis and reanalysis of a high profile Natu...
proteomicsnews.blogspot.com
December 2, 2024 at 2:26 PM
Related - there are whole high profile “protein atlases” based on transcript expression that are clearly inaccurate - proteomicsnews.blogspot.com/2024/06/re-r...
Reposted by Hirak Das
More recently in @rjdlab.bsky.social, we have discovered a new human peroxisomal biogenesis protein and revealed a new paradigm in peroxisomal protein import (www.biorxiv.org/content/10.1...)
PEX39 facilitates the peroxisomal import of PTS2 proteins
Peroxisomes are metabolic organelles essential for human health. Defects in peroxisomal biogenesis proteins (peroxins/PEXs) cause devastating disease. PEX7 binds newly synthesized proteins containing ...
www.biorxiv.org
November 23, 2024 at 5:13 PM
More recently in @rjdlab.bsky.social, we have discovered a new human peroxisomal biogenesis protein and revealed a new paradigm in peroxisomal protein import (www.biorxiv.org/content/10.1...)
Reposted by Hirak Das
This diagram was made by Christine Liu, PhD - creator of two photon art @christineliuart.bsky.social
I think you’ll love it :) @odedrechavi.bsky.social
I think you’ll love it :) @odedrechavi.bsky.social
November 23, 2024 at 12:12 AM
This diagram was made by Christine Liu, PhD - creator of two photon art @christineliuart.bsky.social
I think you’ll love it :) @odedrechavi.bsky.social
I think you’ll love it :) @odedrechavi.bsky.social
Reposted by Hirak Das
My perspective on CVs for DIA-based #proteomics is out in JPR
It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs.
doi.org/10.1021/acs....
It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs.
doi.org/10.1021/acs....
Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics
The coefficient of variation (CV) is a measure that is frequently used to assess data dispersion for mass spectrometry-based proteomics. In the current era of burgeoning technical developments, there ...
doi.org
November 22, 2024 at 9:50 AM
My perspective on CVs for DIA-based #proteomics is out in JPR
It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs.
doi.org/10.1021/acs....
It explores how normalisation, the CV formula and software parameters affect the outputs. It suggests parameters to use for biological and technical studies and provides an R package to calculate CVs.
doi.org/10.1021/acs....
Reposted by Hirak Das
We recently benchmarked multiple packages for #proteomics differential expression analysis. The biggest conclusion is that major differences among tools are only observed in lower-quality datasets. When you see a benchmark, first look into the data that was used. pubs.acs.org/doi/10.1021/...
LFQ-Based Peptide and Protein Intensity Differential Expression Analysis
Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quan...
pubs.acs.org
November 22, 2024 at 7:26 PM
We recently benchmarked multiple packages for #proteomics differential expression analysis. The biggest conclusion is that major differences among tools are only observed in lower-quality datasets. When you see a benchmark, first look into the data that was used. pubs.acs.org/doi/10.1021/...
Reposted by Hirak Das
✨ Exciting news! This year, @pride-ebi.bsky.social introduced a new way to transfer data using the Globus protocol! 🚀
Check out this fantastic 15-minute intro video by @deeptijkundu.bsky.social, PRIDE's lead data curator:
📹 www.youtube.com/watch?v=VRNu...
#DataTransfer #Proteomics #Globus #Faster
Check out this fantastic 15-minute intro video by @deeptijkundu.bsky.social, PRIDE's lead data curator:
📹 www.youtube.com/watch?v=VRNu...
#DataTransfer #Proteomics #Globus #Faster
How to manually upload a proteomics dataset to PRIDE Archive database.
YouTube video by Yasset Perez-Riverol
www.youtube.com
November 19, 2024 at 6:51 PM
✨ Exciting news! This year, @pride-ebi.bsky.social introduced a new way to transfer data using the Globus protocol! 🚀
Check out this fantastic 15-minute intro video by @deeptijkundu.bsky.social, PRIDE's lead data curator:
📹 www.youtube.com/watch?v=VRNu...
#DataTransfer #Proteomics #Globus #Faster
Check out this fantastic 15-minute intro video by @deeptijkundu.bsky.social, PRIDE's lead data curator:
📹 www.youtube.com/watch?v=VRNu...
#DataTransfer #Proteomics #Globus #Faster
Reposted by Hirak Das
The Baker lab seems serious about moving into enzyme design.
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
November 15, 2024 at 10:11 PM
The Baker lab seems serious about moving into enzyme design.
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
Here, they train a flow-matching model that can be conditioned by atomic coordinates and then use it to design enzymes based on active site geometry specified by density functional theory.
www.biorxiv.org/content/10.1...
Reposted by Hirak Das
News in Proteomics Research | Get ultralow flow rate nanoLC with ONE pump?? proteomicsnews.blogs...
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#proteomics #prot-other
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#proteomics #prot-other
November 17, 2024 at 9:40 PM
News in Proteomics Research | Get ultralow flow rate nanoLC with ONE pump?? proteomicsnews.blogs...
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#proteomics #prot-other
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#proteomics #prot-other
Reposted by Hirak Das
Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
January 24, 2024 at 9:00 AM
Autoprot: Processing, Analysis and Visualization of Proteomics Data in Python www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint