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Jan Schejbal

@schejbaljlab.bsky.social
592 followers 559 following 95 posts

Perpetual student of bioanalytical sciences, life and everything. #teamMassSpec and #proteomics Ideas expressed here are solely mine. A girl dad 👨‍👩‍👧‍👧 born and raised in 🇨🇿, living in New England 🇺🇲

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Jan Schejbal @schejbaljlab.bsky.social · 06/05/2025
There should be support for ECRs as well. There are also country specific programs, I know Norway, Sweden and Denmark have recently announced their own programs. Just type in country of interest and keep checking, I assume most of EU countries will announce similar programs this year.
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Jan Schejbal @schejbaljlab.bsky.social · 06/05/2025
EU just pledged €0.5B in research funding to attract and retain talent👇 The initiative is called 'Choose Europe for Science'
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US HUPO @us-hupo.org · 26/02/2025
Thank you for joining us at US HUPO 2025 in Philadelphia! We will see you in St. Louis for US HUPO 2026! #Proteomics #USHUPO2025 #USHUPOConference 🧪
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Jan Schejbal @schejbaljlab.bsky.social · 23/02/2025
Yes!
media.tenor.com
a man in a suit and tie is sitting at a desk in front of a bookshelf .
ALT: a man in a suit and tie is sitting at a desk in front of a bookshelf .
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Jan Schejbal @schejbaljlab.bsky.social · 23/02/2025
How good or bad idea is it to take one week vacation and be dropped the evening before #USHUPO2025 starts (and you lead morning short course 🚀)? Guess we will find out tomorrow. Ping me here or on LinkedIn if you want to chat. I am happy to find time! #Proteomics
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BioMassSpec @realbiomassspec.bsky.social · 30/01/2025
Communicating with Stakeholders to Identify High-Impact Research Directions for Non-Targeted Analysis #AC #MassSpec pubs.acs.org/doi/10.1021/...
pubs.acs.org
Communicating with Stakeholders to Identify High-Impact Research Directions for Non-Targeted Analysis
Non-targeted analysis (NTA) using high-resolution mass spectrometry without defined chemical targets has the potential to expand and improve chemical monitoring in many fields. Despite rapid advancements within the research community, NTA methods and data remain underutilized by many potential beneficiaries. To better understand barriers toward widespread adoption, the Best Practices for Non-Targeted Analysis (BP4NTA) working group conducted focus group meetings and follow-up surveys with scientists (n = 61) from various sectors (e.g., drinking water utilities, epidemiologists, n = 9) where NTA is expected to provide future value. Meeting participants included producers and end-users of NTA data with a wide range of familiarity with NTA methods and outputs. Discussions focused on identifying specific barriers that limit adoption and on setting NTA product development priorities. Stated priorities fell into four major categories: 1) education and training materials; 2) QA/QC frameworks and study design guidance; 3) accessible compound databases and libraries; and 4) NTA data linkages with chemical fate and toxicity information. Based on participant feedback, this manuscript proposes research directions, such as standardization of training materials, that BP4NTA and other institutions can pursue to expand NTA use in various application scenarios and decision contexts.
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Jan Schejbal @schejbaljlab.bsky.social · 15/01/2025
🤔 Ever wondered how proteomics thrives in (bio)pharma🚀? How you could provide impact in industry with proteomics background earned in academia? Please join me and @drawheatcraft.bsky.social for Sunday morning US HUPO 2025 short course 👇
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Jan Schejbal @schejbaljlab.bsky.social · 15/01/2025
We will look at proteomics in pharma industry from multiple angles 🌐How it integrates into the pharma matrix environment. 🎯How it brings impact and propels our knowledge. 🤝How to learn more about proteomics in industry through various forms of employment or collaborations.
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Jan Schejbal @schejbaljlab.bsky.social · 15/01/2025
🤔 Ever wondered how proteomics thrives in (bio)pharma🚀? How you could provide impact in industry with proteomics background earned in academia? Please join me and @drawheatcraft.bsky.social for Sunday morning US HUPO 2025 short course 👇
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PastelBio @pastelbio.bsky.social · 13/01/2025
A Technical Evaluation of Plasma Proteomics Technologies www.biorxiv.org/cont... --- #proteomics #prot-preprint
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Olga Vitek @olgavitek.bsky.social · 12/01/2025
May Institute on Computation and Statistics for Mass Spectrometry and Proteomics @KhouryCollege @Northeastern in Boston MA is happening in person on April 28-May 11, 2025 and is accepting applications! You will not regret attending computationalproteomics.khoury.northeastern.edu
computationalproteomics.khoury.northeastern.edu
May Institute – Computation and statistics for mass spectrometry and proteomics
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Emma Doud @fireinlab.bsky.social · 12/01/2025
The May Institute is a fantastic learning experience and available virtually and in person! #teammassspec #proteomics computationalproteomics.khoury.northeastern.edu
computationalproteomics.khoury.northeastern.edu
May Institute – Computation and statistics for mass spectrometry and proteomics
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Jan Schejbal @schejbaljlab.bsky.social · 12/01/2025
...Looks like I have to force myself finally write that paper on this 😅
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Jan Schejbal @schejbaljlab.bsky.social · 12/01/2025
I also just remembered there was another, scientific, reason. When enriching protein the molar binding capacity is actually lower than when enriching peptides - some binging sites will become inaccessible because they are spatially blocked by the protein size. This was advantageous in our settings.
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
Economic reasons 🙂 the biotynated proteins make up only ~2% of the sample. Digesting enriched fraction resulted in 50fold savings in trypsin cost I think we went from $25k to $500 for one study.
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
Happy to help🙂
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
If those look good and issues prevail, I fall back to some relatively accessible positive control samples to pinpoint the issue. Alternatively you can use antibody against biotin for pull down to bypass streptavidin and check that the sample quality is good. Good luck.
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
That's too difficult to say. I would try with fresh batch of beads and if that doesn't help look for other reasons for failure. IDs are the ultimate read out, it is important to have reliable check points along the way like the yield and protein concentration if the import sample.
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
I discard the non-biotinglated peptides. Too high likelihood that some come from non-specific binding. Unless you need to pool to get over the sensitivity threshold. Even in that case I would only consider hits where there is biotin tag/specific fragment detected on given peptide/protein.
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
Absolutely, just want to mention than in order to optimize the labeling steps it it essential to understand the performance of the pull down and it's reliability (hence the need for positive control like the biotinylated cell lysate or similar).
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Jan Schejbal @schejbaljlab.bsky.social · 11/01/2025
And for elution. We also did on-bead digestion which allows for elution with high acid+ACN steps -> dry down resuspend in LC-MS injection buffer. There are some publications on this. If you tune all steps you can get to >90% peptides biotinylated in the final sample.
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Jan Schejbal @schejbaljlab.bsky.social · 10/01/2025
Can be hard. I would make a rough estimate from the prevalence of the PTM. We have done similar thing where we specifically targeted small % of proteome. A good positive control sample was biotynating HeLa lysate and then mixing it unlabeled HeLa in expected ratios. Allows MD without precious sample
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Jan Schejbal @schejbaljlab.bsky.social · 10/01/2025
Also, I've heard there are some bad batches of streptavidin going around.
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Jan Schejbal @schejbaljlab.bsky.social · 10/01/2025
For us the main optimization factor was carefully matching binding capacity to expected amount of biotinylated protein. Or rather making sure there is more biotinylated protein in the sample then binding capacity. The unspecific binding is basically unwashable.
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Jan Schejbal @schejbaljlab.bsky.social · 04/01/2025
How come this beautiful preprint didn't get much traction in here🤔? We will definitely want to give MAETi a try! Anyone else is planning to try this out? Any words of wisdom from team #proteomics?
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ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 29/12/2024
Do you have a favorite proteomic paper of 2024? I narrowed my list down to 20-ish. (It's pretty clear what Nature had a favorite) proteomicsnews.blogspot.com/2024/12/my-f...
proteomicsnews.blogspot.com
My favorite proteomics papers of 2024!
It's been...a...year....for sure.  And for proteomics, this is EASILY the biggest year ever. Mine kicked off with the honor of being invit...
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Jan Schejbal @schejbaljlab.bsky.social · 29/12/2024
Honestly don't know. I found it in my Google Chrome 'news' feed😁 and since my brain is on vacation this time of the year too I didn't search the source... It looks like it is AI generated based on the YT channel info.
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Jan Schejbal @schejbaljlab.bsky.social · 28/12/2024
I am a proteomicist 🧑‍🔬 nice to meet you 👋 #teammassspec #proteomics youtu.be/b3ImaM7v2OY?...
youtu.be
Proteomics in 2 Minutes
YouTube video by 2 Minute Expert
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Jan Schejbal @schejbaljlab.bsky.social · 20/12/2024
UPDATE: position filled! Thanks everyone for the help🙂
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US HUPO @us-hupo.org · 18/12/2024
We’re thrilled to present "We Are the Analyzers" – an anthem for the proteomics community! A huge shoutout to everyone who brought this incredible song to life. Look what proteomics has already shown us 🎶🧪youtu.be/wzmJDNmsWK8 #Proteomics #USHUPO20YRS
youtu.be
We Are the Analyzers - Proteomics Anthem
We Are the Analyzers - A Proteomics Anthem by US HUPO.
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Jan Schejbal @schejbaljlab.bsky.social · 09/12/2024
Thank you for the shout-out for the short course 😁 really appreciate it! Also @drawheatcraft.bsky.social will co-lead with me, so she deserves a shout-out too! We will do our best not to disappoint the high expectations 😬
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Ben Neely @benneely.com · 06/12/2024
The next season of #THEProteomicsShow has started! For The Philly Express, @proteomicsnews.bsky.social and I will feature speakers at #USHUPO2024 (weekly, hopefully). This first episode was the agenda, cause it was a bad idea the last two times. Enjoy!
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ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 06/12/2024
Spatial proteomics is Nature's Method of the Year for 2024!! Congrats to the great people in our field featured in this virtual issue! www.nature.com/articles/s41...
nature.com
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.
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Rong Fan @rongfan8.bsky.social · 07/12/2024
SPATIAL PROTEOMICS is the Method of the Year 2024!!! 🤩🤩🤩 www.nature.com/articles/s41...
nature.com
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.
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Jan Schejbal @schejbaljlab.bsky.social · 04/12/2024
The position has been filled 😊 Thank you to all who boosted the signal and helped us find the great candidate. If anyone wants to peak behind the veil of the hiring process, my DMs are open.
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Jan Schejbal @schejbaljlab.bsky.social · 03/12/2024
I loved this episode🤩! We need to discuss the 'good enough' proteomics more (partly because that's the best I can do 😅). Accessibility is the key right now. We are moving in the right direction but further progress is so important.
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Jan Schejbal @schejbaljlab.bsky.social · 03/12/2024
Got it... Actually, if you know of labs with immunopeptidomics focus and good grad students in US, please let me know. I would like to share the opening with them directly. Thanks!
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Jan Schejbal @schejbaljlab.bsky.social · 02/12/2024
I just realized, I worded it poorly. My team is actually looking for an intern.
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Jan Schejbal @schejbaljlab.bsky.social · 26/11/2024
Here is couple: bsky.app/profile/ajbr... And @benneely.com has great Proteomics feeds set up🙂
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US HUPO @us-hupo.org · 22/11/2024
📣 Attention #USHUPO2025 submitters! 📣 All abstract disposition notices have been sent out! 🎉🎉🎉 Please check your inbox for updates. #USHUPO
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Alejandro Brenes @ajbrenes.com · 18/11/2024
#TeamMassSpec recent newcomers you'll want to follow: @jespervolsen.bsky.social @kmechtler.bsky.social @vadim-demichev.bsky.social @nesvilab.bsky.social @nlkproteomics.bsky.social
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PastelBio @pastelbio.bsky.social · 18/11/2024
UniProt: the Universal Protein Knowledgebase in 2025 academic.oup.com/nar... --- #proteomics #prot-paper
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Jan Schejbal @schejbaljlab.bsky.social · 18/11/2024
Few quick notes for new followers 🦋 Please add some bio ✍️ before starting to follow. I still have time to go through new followers and skip those without bio just as a precaution. If you add it later, I (and others) may not return to follow back and I would hate to miss out on great scientists👩‍🔬🧑‍🔬!
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Jan Schejbal @schejbaljlab.bsky.social · 18/11/2024
This is just insane 🤯 Also, I need to learn to properly cite blog posts 🫣
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Razvan Borza @rborza.bsky.social · 17/11/2024
⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️ 🔄Share to help people finding its topic/field - STRUCTURAL BIOLOGY Structural Biology 1: bsky.app/starter-pack... Structural Biology 2: bsky.app/starter-pack... Crystallography: bsky.app/starter-pack... Synchrotron&CryoEM: bsky.app/starter-pack...
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Jan Schejbal @schejbaljlab.bsky.social · 17/11/2024
Non-science: November 17 marks the 35th anniversary of Velvet Revolution in my home country 🇨🇿 The freedom to travel, study and do what you love is not given and can be taken away. Let's not forget. Truth and love must prevail over lies and hatred (Václav Havel ✌️) #dikyzemuzem
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Alejandro Brenes @ajbrenes.com · 16/11/2024
Here's a new list for early career researchers (=not had your own lab for ages) in proteomics. Feel free to ask to be added or removed, I've tried to make a guess but could've got it wrong. I think it's good to also have an ECR network. #teamMassSpec go.bsky.app/Dp8PHX1
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Ben Neely @benneely.com · 16/11/2024
As of right now, it is not an exaggeration that I am getting many fold better science/proteomics content and interactions here, as well as some of my pop culture (eventually sports) and local info! A good time to get mine folks that *you* make the algorithm. bsky.social/about/blog/7...
bsky.social
Algorithmic Choice with Custom Feeds - Bluesky
Our implementation of algorithmic choice lets users customize one of the most important parts of their social media experience: their feed.
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Matthias Nau @matthiasnau.bsky.social · 30/10/2024
Want to make beautiful scientific figures? Easy! The NIH released a library of 2000+ free scientific illustrations called *BioArt*. Check it out! bioart.niaid.nih.gov #AcademicSky #PsychSciSky 🧠🟦 🧪
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Ben Neely @benneely.com · 15/11/2024
This week’s episode of #THEProteomicsShow, with me and @proteomicsnews.bsky.social, had Ilaria Piazza on and featured a lot of structural proteomics and the normal fun convo as we continue to ask “What is a proteomics?”. Find it wherever you find fine podcast. Enjoy!
Newest episode of the proteomics show. Can be found anywhere, even here https://open.spotify.com/show/3R8aGNVMKwfovkWWRVnu4E
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