Bharath Nair (ഭരത് നായർ)

Vladimir Gorshkov manage to put in place the first release for #ThermoRawFileParser (TRFP) with dotnet support, not need for mono anymore. This is TRFP 2.0dev, if you are using this tool, please test/test, we want to release 2.0 including #bioconda and #biocontainer github.com/CompOmics/Th...

Looking for feedback. How do you guys does feature intensity normalization? Median across entire experiment? Median by sample, it depends of the experiments?

Struggling to compare Bruker timsTOF methods or extract window schemes from raw .d files? I developed a free desktop tool to solve this: timsCompare! 🚀

It automates the manual work of extracting method parameters, presenting them in a structured and comparable view.

(A thread 🧵)

www.nature.com/articles/d41...

lol what?
This just tells me how bad Marriott's reading and media consumption habits are, because it feels like more academics are doing public scholarship than ever!
Maybe they're not all "Great White Scholar" types, but they're there, and doing the work.

Alright, help from my "wider" mass tolerance peeps ( @pwilmarth.bsky.social @ypriverol.bsky.social @michaellazear.bsky.social): I have confirmed what you all said that 1.25 Da MS1 and 20 ppm MS2 is a winning DDA combination. But I see in MSFragger I can do an upper and lower. Do +- 1.25 Da on MS1?

While journal publishing has always been deeply problematic, hurting both the pace and trajectory of science, something is happening in this moment that is finally causing the system to crumble under its own weight and cost.
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Archaeology Lab Technician Job at Durham University | HigherJobz Apply now for Archaeology Lab Technician at Durham University, UK. Full-time permanent role in Archaeology. Deadline: 17 Sept 2025.

Advanced Technician (Archaeological Laboratories) – Durham University, UK
Permanent archaeology lab technician role
Eligibility: Degree in Archaeology
Deadline: 17 Sept 2025
Details: higherjobz.com/archaeology-...

#AcademicJobs #ArchaeologyCareers #UKJobs #PermanentRole #ResearchJobs

Congrats 🎉

Chuffed to have participated in the Nordic Conference on Mass Spectrometry and Proteomics 2025 in Odense - "the birth place of proteomics". Also, massive congrats to Amalie to winning the Best Poster Award. @markersofpollution.bsky.social - grateful for the support!

Machine Learning for Multi-Omics Integration 15-17 December 2025 Dept. Evolutionary Biology, Ecology & Environmental Sciences Faculty of Biology, University of Barcelona Institut de Recerca de la Biodiversitat (IRBio) Av. Diagonal, 643, Les ...

We would like to inform you that only four seats are left for the in-person course, “Machine Learning for Multi-Omics Integration,” with @oskolkov.bsky.social taking place on 15–17 December at the University of Barcelona @irbio-ub.bsky.social

www.physalia-courses.org/courses-work...

Symposia - SMBE 2026 - Copenhagen Denmark SMBE 2026 Symposia Check deadlines and important dates below.  Days Hours Minutes Seconds Conference Symposia We are now accepting proposals for symposium for the 2026 Annual meeting taking place in Copenhagen, Denmark. Selection of proposals will prioritize the interests of SMBE members, emphasizing innovative scientific developments while ensuring geographic and gender diversity among the participants. […]

The SMBE 2026 Annual Meeting in Copenhagen is open for symposium proposals from Sept 1 to Oct 15, 2025. Details at https://smbe2026.org/symposia/. Looking forward to your submissions! #conference

YouTube video by PAASTA community PAASTA Seminar Series - Ioannis Patramanis

Following a marvelous time at ISBA11 and our PAASTA conference, we're back to sharing the work of our community with you here!

@ipatramanis.bsky.social PAASTA talk from March about PaleoProPhyler a tool for #phylogenies from ancient proteins is now live on our YouTube youtu.be/2gVEQyinL4A

More than 500 international scholars attended ISBA 11. Here are many of them looking up at the camera in a large group shot

Thanks to @isbarchaeology.bsky.social and @isba11.bsky.social for a great conference.

I mentioned the legacy of Henk Kars of VU who established ISBA

Geoarchaeology closed. Here is the link to the petition to save Earth Sciences @vuamsterdam.bsky.social

www.change.org/p/red-aardwe...

Picture of the roll-up presenteing PCI Archaeology during the congress, and of the ISBA11 tote bag.

PCI Archaeology was at @isba11.bsky.social in Turin last week! Stay tuned for new #openaccess biomolecular papers soon with full transparency in the editorial process!

Thank you @matthewcollins.bsky.social and Marta Arzarello for sharing our initiative!
@isbarchaeology.bsky.social 🧪🏺🦣

Fun working with @archaeosheep (not on bsky yet... xD) @isma-rgz.mastodon.social.ap.brid.gy and @drsambrown.bsky.social. Do check it out!!!

[ASAP] Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00179

(JASMS) [ASAP] Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00179 (RSS) #MassSpecRSS #JASMS

⬇️⬇️⬇️
Also worth reading for other domains than health sciences! 👏

Ancient microbial DNA and proteins preserve in concretions covering human remains Microbiome; Omics; Proteomics; Archeology

🚨Thrilled to share our new paper!!
We were able to retrieve ancient DNA and proteins from layers of sediment attached to the skeletal remains of individuals from a Neolithic site from Southern Italy 💀🧬🦠
www.cell.com/iscience/ful...

Do not trust AI or ChatGPT-5 to do the most basic things like labeling a picture of the hydrologic cycle. Here's what it gave me.
(Evaporation arrow pointing into the ground. Both surface water and the "ocean" labels underground. Transpiration arrow coming from the #water surface, not plants...]

Our distant ancestors sometimes did things tens or hundreds of thousands of years ago, leaving incidental traces that we sometimes are lucky enough to notice. Whatever they were doing, it was almost certainly not their intention to be noticed by us.

Registration deadline is TOMORROW! 🍝 🏺

Richard Seymour · Baseline Communism: David Graeber’s Innovations In his critique of economics, as in his philippic against ‘bullshit jobs’, Graeber stresses the political decisions...

‘Graeber is at his most speculative, and engaging, as a theorist-practitioner of fun.’

@leninology.bsky.social reads David Graeber’s essays: www.lrb.co.uk/the-paper/v4...

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results FragPipe is recognized as one of the fastest computational platforms in proteomics, making it a practical solution for the rapid quality control of high-throughput sample analyses. Starting with version 23.0, FragPipe introduced the “Generate Summary Report” feature, offering .pdf reports with essential quality control metrics to address the challenge of intuitively assessing large-scale proteomics data. While traditional spreadsheet formats (e.g., tsv files) are accessible, the complexity of the data often limits user-friendly interpretation. To further enhance accessibility, PSManalyst, a Shiny-based R application, was developed to process FragPipe output files (psm.tsv, protein.tsv, and combined_protein.tsv) and provide interactive, code-free data visualization. Users can filter peptide-spectrum matches (PSMs) by quality scores, visualize protease cleavage fingerprints as heatmaps and SeqLogos, and access a range of quality control metrics and representations such as peptide length distributions, ion densities, mass errors, and wordclouds for overrepresented peptides. The tool facilitates seamless switching between PSM and protein data visualization, offering insights into protein abundance discrepancies, samplewise similarity metrics, protein coverage, and contaminants evaluation. PSManalyst leverages several R libraries (lsa, vegan, ggfortify, ggseqlogo, wordcloud2, tidyverse, ggpointdensity, and plotly) and runs on Windows, MacOS, and Linux, requiring only a local R setup and an IDE. The app is available at (https://github.com/41ison/PSManalyst.

It's now properly published. If you want to easily check important characteristics of your data before diving into complicated statistics, check out PSManalyst.

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

🎉🎉🎉

Paleoproteomics in Atapuerca - Diálogos Sapiens - Sapiens Dialogues - Podcast on iVoox Listen and download Diálogos Sapiens - Sapiens Dialogues episodes for free. 22nd episode of Sapiens Dialogues. This is the fourth dialogue of the fourth season. The paleoproteomics specialist Prof. Ma...

I had the opportunity to interview @matthewcollins.bsky.social on his recent visit to @cenieh.bsky.social. The podcast is out now! It's a fun chat about #palaeoproteomics and the ways we can study ancient #proteins at Atapuerca! Thanks Matthew for the chat! www.ivoox.com/en/paleoprot...

Nordic MSP 2025 – Mass Spectrometry & Proteomics Conference in Odense Join leading scientists at Nordic MSP 2025 at ODEON in Odense, Denmark. A premier conference on mass spectrometry and proteomics.

The last day for registering for the Nordic Conference in Mass Spectrometry and Proteomics 2025 in Odense, Denmark, 1-3rd September 2025, is closing in. Please sign up before Friday!
www.nordicmsp2025.com

Characterizing and engineering PTMs with high throughput systems (not mass spectrometers!)   Disclaimers! I've had this open on my desktop since I got back from vacation and I do not get it. We're way way out of my wheelhouse.  I...

News in Proteomics Research blog post | Characterizing and engineering PTMs with high throughput systems (not mass spectrometers!) proteomicsnews.blogs...

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#proteomics #prot-other

Kerala Is Still the Stronghold of India’s Communist Movement Narendra Modi’s government is aggressively hostile to the communist-led left-wing alliance that holds power in Kerala because it has a remarkable track record of improving living standards for its people, unlike Modi and his Hindutva cronies.

Narendra Modi’s government is aggressively hostile to the communist-led left-wing alliance that holds power in Kerala because it has a remarkable track record of improving living standards for its people, unlike Modi and his Hindutva cronies.