Discover and read the best of Twitter Threads about #proteomics
Most recents (21)
In #NextGenerationProteomics news, today we cover the basics of Proximity ligation assay (PLA) technology, also known as proximity barcoding assay technology, which is a method for detecting protein-protein interactions in cells or tissues.
The assay is based on the principle of ligating two probes (such as antibodies) that are in close proximity to each other, typically within a few nanometers. The ligation reaction produces a circular DNA molecule that is amplified by polymerase chain reaction (PCR) and
can be detected by sequencing or by fluorescence-based microarray readouts. The technology allows for the quantification of specific protein interactions in complex biological samples and can be used for a variety of applications, including drug discovery,
1. #Bioinformatics is the application of #computational techniques to the #analysis of #biological #data, such as #sequences, #structures, and #interactions, and is an essential field of modern biology and medicine.
2. #Bioinformatics has many exciting applications in various fields, such as #genetics, #genomics, #proteomics, and #metabolomics, that can provide new insights into the workings of living systems, and can help to advance science and society.
🧬🧵here is a Twitter thread explaining #Bioinformatics in simple terms:🧬🧵
#Bioinformatics is the field that uses computational tools and methods to analyze and interpret #biological #data.
This can include analyzing #DNA and #protein #sequences, predicting the structure and function of #molecules, and modeling biological systems.
1) Welcome to our new #accredited #tweetorial on the Pathophysiology of #DKD in #T2D: Traditional Teaching and New Insights. Our expert author is Hans-Joachim Anders, MD, @hjanders_hans from @LMU_Uniklinikum of @LMU_Muenchen 
2) This #accredited #tweetorial series on the foundations of #kidneydisease #DKD through the lens of #T2D is supported by an independent educational grant from the Boehringer Ingelheim/Lilly Alliance and is intended for healthcare providers.
3) This activity is accredited for #physicians #physicianassociates #nurses #NPs #pharmacists. Past programs still eligible for credit can be found at ckd-ce.com. Faculty disclosures & accreditation statement are at ckd-ce.com/disclosures/. FOLLOW US!
Our latest now out @NatureComms! We use cell surface #proteomics to find new #immunotherapy targets and biomarkers of resistance in #myeloma #mssm. Resource + we identify CCR10 as target & develop natural ligand CAR-Ts. Huge effort led by @idferguson
nature.com/articles/s4146…
nature.com/articles/s4146…
w/informatics & primary sample analysis led by @bonellpatinoe. Wonderful collaboration with @realjimwells @j_eyquem @iamdrdex and our @ucsfcancer myeloma clinical team @ninashah33 @tombmt133 @myelomawolf @sandywong0211
We initially quantified >1000 membrane spanning proteins across myeloma cells and identified some surprising proteins that most distinguish plasma cells vs. B-cell leukemia, along with canonical markers
Mass Spec-based #proteomics is such an exciting field. Here is a brief🧵of some great developments focusing on depth/speed
The term proteome appeared in 95/96 science.org/doi/10.1126/sc… https://t.co/6eij4axDzy and (rumors in Australia) coined by Marc Wilkins and co-workers 1/13
The term proteome appeared in 95/96 science.org/doi/10.1126/sc… https://t.co/6eij4axDzy and (rumors in Australia) coined by Marc Wilkins and co-workers 1/13
Let’s start in 1996 where @labs_mann built on work by Watanabe and co-workers to identify ~150 proteins from yeast 2/13 pnas.org/doi/full/10.10…
Jumping to 2001, @JohnRYatesIII introduced multidimensional protein identification technology (MudPIT) and identified ~1.5K proteins from yeast. 3/13 nature.com/articles/nbt03…
Our paper is out!
Optimized Glycopeptide Enrichment Method–It Is All about the Sauce pubs.acs.org/doi/10.1021/ac…
#glycotime #TeamMassSpec #proteomics
A personal note (and couple of comments about publishing methods): \start
Optimized Glycopeptide Enrichment Method–It Is All about the Sauce pubs.acs.org/doi/10.1021/ac…
#glycotime #TeamMassSpec #proteomics
A personal note (and couple of comments about publishing methods): \start
I really like this project, mainly because what it represents for me. I'm a scientist at a proteomics service facility led by @YishaiLevin. We're a bunch of talented scientists (if I might say so..), and our job,
in my opinion, is to enable excellent science through excellent proteomics. Enabling science is not only performing the experiments, but also making sure our capabilities are top-notch. This means investing in R&D of methods, and this is how this project was born:
The London stock market is now closed and $ONT.L Oxford @nanopore is presenting technology updates. I'll live tweet my highlights, but won't be thoroughly complete with screenshots (thread)
My COIs bit.ly/avilcoi
First talk is James Clark for Platform updates.
1) Welcome to our new #accredited #tweetorial on the Pathophysiology of #DKD in #T2D: Traditional Teaching and New Insights. Our expert author is Hans-Joachim Anders, MD, @hjanders_hans from @LMU_Uniklinikum of @LMU_Muenchen
2) This #accredited #tweetorial series on the foundations of #kidneydisease #DKD through the lens of #T2D is supported by an independent educational grant from the Boehringer Ingelheim/Lilly Alliance and is intended for healthcare providers.
3) This activity is accredited for #physicians #physicianassociates #nurses #NPs #pharmacists 🇺🇸🇪🇺🇬🇧🇨🇦. Past programs still eligible for credit are at ckd-ce.com. Faculty disclosures are at ckd-ce.com/disclosures/. FOLLOW US for regular programs by expert faculty!
In a recent lung cancer pilot study, we identified and quantified a record number of 13,187 protein groups with our next-generation single-shot proteomics technology HRM.
This was achieved using FAIMS-DIA with highest resolution chromatography and FAIMS Exploris 480. (1/n)
This was achieved using FAIMS-DIA with highest resolution chromatography and FAIMS Exploris 480. (1/n)
The depth of analysis was superior to the one achieved in the Deep Human Proteome Atlas (deep fractionated tissue with multiple MS acquisitions, Wang et al., 2019, Mol Syst Biol).
Comprehensively, we could identify 414 oncogenes, 392 transcription factors, 837 plasma membrane proteins (25 GPCR), and 316 kinases covering a dynamic range of 10. In addition, 0.25 Mio peptides (including modifications) were measured in totality.
Very happy to present our #proteomics analysis of #lungcancer published today @NatureCancer!🙂
Here’s a walk-through: #MassSpec analysis covering almost 14k proteins in 141 NSCLC tumors revealed 6 proteome subtypes with distinct biology. 1/6
rdcu.be/cBOtU
Here’s a walk-through: #MassSpec analysis covering almost 14k proteins in 141 NSCLC tumors revealed 6 proteome subtypes with distinct biology. 1/6
rdcu.be/cBOtU
#NSCLC proteome subtypes are driven by histology, growth pattern, immune cell infiltration, driver mutations, oncogenic pathways, and cell types, suggesting potential clinical value for treatment stratification and #PrecisionMedicine. 2/6
Unexpectedly, #proteogenomics analysis revealed that high neoantigen burden was linked to global hypomethylation, and that complex neoantigens mapping to genomic regions normally not active in lung were produced in immune-cold subtypes. 3/6
Many thanks to the awesome ladies at @IWS_Network for the chance to share my #immigrant #womanofcolour #womaninscience👩🏽🔬story throughout this week as part of their Voices Without Frontiers program!
iwsnetwork.ca/voices-without…
#IWSvoices #WomenInSTEM
iwsnetwork.ca/voices-without…
#IWSvoices #WomenInSTEM
I was born in #Guyana 🇬🇾
➡️ Amerindian name meaning “Land of Many Waters”.
➡️small in size (<800, 000 people), rich in natural resources
➡️only English-speaking country in South America
➡️Diversity of people with amazing cultural mix @IWS_Network #VoicesIWS #WomenInSTEM
➡️ Amerindian name meaning “Land of Many Waters”.
➡️small in size (<800, 000 people), rich in natural resources
➡️only English-speaking country in South America
➡️Diversity of people with amazing cultural mix @IWS_Network #VoicesIWS #WomenInSTEM
Genetically I’m Indian - ancestors brought to ‘British Guiana’ from India during colonial times to work on #sugarplantations.
Culturally I’m #Caribbean as #Guyana shares historical and cultural ties with other Anglo-Caribbean countries.
@IWS_Network #VoicesIWS #WomenInSTEM
Culturally I’m #Caribbean as #Guyana shares historical and cultural ties with other Anglo-Caribbean countries.
@IWS_Network #VoicesIWS #WomenInSTEM
As promised, a 🧵 to convince you to consider SP4 for your next #proteomics sample prep!
TL;DR: Cell lysate -> pure peptides ready for LC-MS with 20-30 min handling time w/o any filters (FASP, iST, S-Trap) or specialist beads (SP3). 1/n
biorxiv.org/content/10.110… @biorxivpreprint
TL;DR: Cell lysate -> pure peptides ready for LC-MS with 20-30 min handling time w/o any filters (FASP, iST, S-Trap) or specialist beads (SP3). 1/n
biorxiv.org/content/10.110… @biorxivpreprint
Starting off a lab (babraham.ac.uk/our-research/s…) where proteomics was going to be a major approach, our first recruit—postdoc @HarveyEJohnston—set off to craft our work-horse sample prep work-flow.
2/n
2/n
This workflow needed to be: (1) quick-ish; (2) cheap-ish; (3) versatile & scalable (e.g., different sample amounts & vols); (4) able to clean up detergents; (5) compatible with #PTM enrichment approaches (especially #ubiquitin TUBEs & diGly); (3) easy to teach to students.
3/n
3/n
Daily Bookmarks to GAVNet 09/26/2021 greeneracresvaluenetwork.wordpress.com/2021/09/26/dai…
Peznt Journalist on Twitter and ThreadReader
threadreaderapp.com/thread/1440783…
#FutureTrends #predictions #WorldEconomicForum #control #power
threadreaderapp.com/thread/1440783…
#FutureTrends #predictions #WorldEconomicForum #control #power
Single-cell proteomics takes centre stage
nature.com/articles/d4158…
#proteomics #SingleCells #transcriptomics
nature.com/articles/d4158…
#proteomics #SingleCells #transcriptomics
In the #biotech #stocks #NGS field, there is a company that's recently IPOed and has now presented an update of their plans: $OMIC Singular Genomics @SingularGenomi1 investor.singulargenomics.com/static-files/0…
Their two planned instruments, the G4 and the PX, look physically a lot like competitors to the #Illumina NextSeq and NovaSeq, or the #MGI #DNBSEQ G400 and T7 instruments. But the PX is more of a multi-omics play rather than a higher throughput #NGS machine.
It seems we are about 1 year or 1.5 years away from Early Access / Commercial Launch for the PX, maybe around 6 months earlier for the G4 instrument.
Vector-based SARS-CoV2 #vaccines have been associated with vaccine-induced thrombotic thrombocytopenia #VITT/#TTS. It is known that similar to HIT, anti-PF4 antibodies are formed which activate platelets therefore eventually leading to serious thrombosis: nature.com/articles/s4158…
This serious and sometimes fatal condition has been described for both vector-based SARS-CoV2 vaccines ChAdOx1 nCoV-19 (AstraZeneca) and in less frequency for Ad26.COV2.S (Johnson&Johnson). However, it is still unclear why there are large differences in the incidence of #VITT.
To tackle this question, we dropped everything else and compared both vaccines in our local, highly interdisciplinary multi-expertise group from @uni_greifswald, @UMGreifswald and @Loeffler_News: #GreifswalderForscher
Is it possible to predict signaling in single cell? 🤔
Our @attila_gbr with Marco Tognetti, @BodenmillerLab group, @tanevski, and @Sagebio designed a @DR_E_A_M challenge to crowdsource this question and our manuscript is out 🎊biorxiv.org/content/10.110…. Here is what we learnt🧑🎓
Our @attila_gbr with Marco Tognetti, @BodenmillerLab group, @tanevski, and @Sagebio designed a @DR_E_A_M challenge to crowdsource this question and our manuscript is out 🎊biorxiv.org/content/10.110…. Here is what we learnt🧑🎓
we used this biorxiv.org/content/10.110… rich dataset from the @BodenmillerLab and @Picotti_Lab labs: 80 millions of #singlecell from 67 #breastcancer cell lines, 36 measured markers, 5 kinase inhibitors, time courses #CyTOF + #proteomics , transcriptomics and genomics
Did the antibody stop working or you cannot measure a node? We can predict it’s activity from other measured nodes. Predictions correlate strongly with test data and are accurate across time and conditions. Watch out for rare signaling patterns though.
JPM Healthcare Daily Roundup #JPM2021
The first day of the conference hasn't disappointed, especially if you're a fan of talking cubes. What is this mysterious object and what sorcery is inside?
See disclosures at the end.
The first day of the conference hasn't disappointed, especially if you're a fan of talking cubes. What is this mysterious object and what sorcery is inside?
See disclosures at the end.
The Tempus One, meant to be carried in a doctor's coat or sat at the bedside, is a physical manifestation of @TempusLabs' genomic and phenotypic data-lake. Oncologists can ask One all sorts of questions regarding their patients, though I'm unsure if it'll (...)
(...) just reflex you to a computer after a sufficiently difficult question. I'm sure we'll learn more soon. Has this sort of form-factor been tried before?
I'm just hoping it has adjustable humor/honesty settings like TARS from Interstellar.
Moving right along.
I'm just hoping it has adjustable humor/honesty settings like TARS from Interstellar.
Moving right along.
Who the hell is naming these proteins? #science
🚨Update🚨
Apparently the protein was 1st published in Feb. 1998 by Wolff et al,they called it "Strabismus", a condition which “a disorder of vision due to a deviation from normal orientation of one or both eyes” and is the medical term for ‘cross-eyed’"
bit.ly/3mmBrMU
Apparently the protein was 1st published in Feb. 1998 by Wolff et al,they called it "Strabismus", a condition which “a disorder of vision due to a deviation from normal orientation of one or both eyes” and is the medical term for ‘cross-eyed’"
bit.ly/3mmBrMU
Another group published the same protein in September of same year (1998) and called it Van Gogh for whatever reason. A footnote was added which said "We have determined that Van Gogh is allelic to strabismus"
genetics.org/content/150/1/…
genetics.org/content/150/1/…
Immensely proud of bring of bringing some important aspects of #precision #proteomics to @NatureRevGenet with @ksuhre @markmccarthyoxf covering #gwas #pqtls and more nature.com/articles/s4157… @scilifelab @KTHresearch @ProteinAtlas
We provide insights into procedures, challenges, considerations and opportunities when combing #genetics and #proteomics for more informed, large scale studies of the circulating #proteome . #biobanks #olink #somalogic #massspec #affinityproteomics #epitopes #causality
Am very grateful to @ksuhre and @markmccarthyoxf for joining in on this journey and making this a wonderful experience over three continents, timezones, project and travel schedules!
A true gem among #multiomics preprints: Integrative Network Fusion by @MarcoChierici, @nicole_bussola, @viperale, et al:
✓ 3 TCGA cancers & simulated data
✓ cross-validation described in detail
✓ flow diagram
✓ source code & data shared
✓ packages w/ version, cited
/n
✓ 3 TCGA cancers & simulated data
✓ cross-validation described in detail
✓ flow diagram
✓ source code & data shared
✓ packages w/ version, cited
/n
- [the method description & comments follows]
- link: biorxiv.org/content/10.110…
- licence the above figures/tables: CC BY-NC-ND 4.0
- an earlier version of INF was previously presented in 2018: doi.org/10.1186/s13062…
- this is the first tweet in #SundayMultiOmics series
- link: biorxiv.org/content/10.110…
- licence the above figures/tables: CC BY-NC-ND 4.0
- an earlier version of INF was previously presented in 2018: doi.org/10.1186/s13062…
- this is the first tweet in #SundayMultiOmics series
[[Introduction]]: Similarity network fusion (SNF, doi.org/10.1038/nmeth.…) is a popular technique (600+ citations, a lot for multi-omics!) for getting a sort of consensus signal from multiple omics; it requires the same patients (less commonly - observations) in each omic.
