Peer Bork was the first “household name” I encountered in bioinformatics research. His paper predicting drugs’ shared targets based on similarity of their side effects has come up at least once a year in my career. We lost a great node in our network today.

Measuring the value and impact of UniProt Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to €5,475 per user.

New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information.

Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.

www.ebi.ac.uk/about/news/a...

We are excited to introduce ‘time’ as a new domain for proteomics multiplexing!

It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA

Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀

A new dimension for multiplexing mass spec analysis -- time -- is enabling scaling up throughput at new levels.

We demonstrate 27-plex DIA enabling over 500 samples / day.

We project that timePlex will enable throughputs exceeding 1,000 samples / day.

www.biorxiv.org/content/10.1...

Diagram comparing processes for creating standard vs. notebook pubs where notebook pubs cut out significant manual, irreproducible editing steps.

We're trying a new publication format — the notebook pub!

By turning our Jupyter Notebooks into publishable artifacts, we hope to share faster, reduce the effort to convert analysis ➡️ pub, and make our work more reproducible.

Weigh in on our commentary:
research.arcadiascience.com/pub/perspect...

Was a great pleasure to write this perspective on two transformative works by leading single-cell proteomics labs. LC-MS now enables to quantify ~6000 proteins per HeLa cell. I think many types of experiments will benefit from being augmented with single-cell proteomics measurements.

A range of features identified from sparse autoencoders trained on different layers on ESM2-650M

This might be the best paper on applying sparse autoencoders to protein language models. The authors identify how neural networks trained on amino acid sequences "discover" different features, some specific to individual protein families, other for substructures

www.biorxiv.org/content/10.1...

Image shows a drop down menu and search results page. It also repeats the text: Wayback Machine Collection Full Text Search Visit web.archive.org Scroll to 🔎Collection Search section Select "End Of Term (US Gov 2024)" from the menu Type in your query term and click search

How to Access the EOT Web Archives

Visit web.archive.org
Scroll to 🔎Collection Search section
Select "End Of Term (US Gov 2024)" from the menu
Type in your query term and click search

Or download bulk WARC files from eotarchive.org/data/
#EOT2024 #EOTArchive

This rate of validation suggests that antibodies should be considered non-specific until proven otherwise:

357 validated out of 1,124 tested.

.

Cell Storage Conditions Impact Single-Cell Proteomic Landscapes Single cell transcriptomics (SCT) has revolutionized our understanding of cellular heterogeneity, yet the emergence of single cell proteomics (SCP) promises a more functional view of cellular dynamics. A challenge is that not all mass spectrometry facilities can perform SCP, and not all laboratories have access to cell sorting equipment required for SCP, which together motivate an interest in sending bulk cell samples through the mail for sorting and SCP analysis. Shipping requires cell storage, which has an unknown effect on SCP results. This study investigates the impact of cell storage conditions on the proteomic landscape at the single cell level, utilizing Data-Independent Acquisition (DIA) coupled with Parallel Accumulation Serial Fragmentation (diaPASEF). Three storage conditions were compared in 293T cells: (1) 37 °C (control), (2) 4 °C overnight, and (3) −196 °C storage followed by liquid nitrogen preservation. Both cold and frozen storage induced significant alterations in the cell diameter, elongation, and proteome composition. By elucidating how cell storage conditions alter cellular morphology and proteome profiles, this study contributes foundational technical information about SCP sample preparation and data quality.

Our first single cell proteomics paper is online now in JPR. A practical story and practice for the biological studies to come next pubs.acs.org/doi/10.1021/...

I am thrilled that this transition finally happened. Goodbye aspirational collection of bookmarks, I read some of you.

I’m going to use Fig 1 of this PNAS article in my very next graduate biostatistics lecture