Claire Eyers

Back by popular demand - it's the time of year when apples, pears and quinces need to be cooked with large quantities of sugar..so I give you Crab Apply Jelly and Membrillo. That's Christmas sorted!

UK ‘falling short’ in fight against rise of superbugs resistant to antibiotics Antimicrobial resistance contributing to estimated 35,000 deaths a year in UK, and government ‘a long way’ from containing the problem, says NAO

In UK, antibiotic-resistant bacterial infections in humans have INCREASED by 13% since 2018…

Despite a target to reduce them by 10%.

www.theguardian.com/society/2025...

Postdoctoral research associate position available in my lab #proteomics as part of a great collaboration with Cathy Merry defining formation and function of #GAGs #proteomics my.corehr.com/pls/ulivrecr...

You know it!

Well this is how to make use of an old prison! @malmaison.bsky.social

Huge congratulations to Professor Andy Levers who has been awarded an OBE for services to industry and the economy in the 2025 New Year Honours list 🎉

Find out more: news.liverpool.ac.uk/2024/12/30/p...

a dog is standing on a table in front of a christmas tree and a fireplace ALT: a dog is standing on a table in front of a christmas tree and a fireplace

In case there was any doubt - teething puppies and Christmas do not work well together.

Check out Amie’s sea lion paper and her supplemental cover out now!! Congratulations @amiesolosky.bsky.social !! pubs.acs.org/doi/10.1021/...

Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation Quantitative analysis of proteomics data frequently employs peptide-identity-propagation (PIP) — also known as match-between-runs (MBR) — to increase the number of peptides quantified in a given LC-MS/MS experiment. PIP can routinely account for up to 40% of all quantitative results, with that proportion rising as high as 75% in single-cell proteomics. Therefore, a significant concern for any PIP method is the possibility of false discoveries: errors that result in peptides being quantified incorrectly. Although several tools for label-free quantification (LFQ) claim to control the false discovery rate (FDR) of PIP, these claims cannot be validated as there is currently no accepted method to assess the accuracy of the stated FDR. We present a method for FDR control of PIP, called “PIP-ECHO” (PIP Error Control via Hybrid cOmpetition) and devise a rigorous protocol for evaluating FDR control of any PIP method. Using three different datasets, we evaluate PIP-ECHO alongside the PIP procedures implemented by FlashLFQ, IonQuant, and MaxQuant. These analyses show that PIP-ECHO can accurately control the FDR of PIP at 1% across multiple datasets. Only PIP-ECHO was able to control the FDR in data with injected sample size equivalent to a single-cell dataset. The three other methods fail to control the FDR at 1%, yielding false discovery proportions ranging from 2–6%. We demonstrate the practical implications of this work by performing differential expression analyses on spike-in datasets, where different known amounts of yeast or E. coli peptides are added to a constant background of HeLa cell lysate peptides. In this setting, PIP-ECHO increases both the accuracy and sensitivity of differential expression analysis: our implementation of PIP-ECHO within FlashLFQ enables the detection of 53% more differentially abundant proteins than MaxQuant and 146% more than IonQuant in the spike-in dataset. ### Competing Interest Statement The authors have declared no competing interest.

Re-posting our new preprint on match between runs. This multi-lab effort (Keich, Noble, Payne & Smith) led by Alex Solivais should be of interest to anyone doing LFQ. We describe here how to control FDR in LFQ and provide the open source software to do it.
www.biorxiv.org/content/10.1...

Hi #TeamMassSpec! #FeMS+ has joined BlueSky! Please share and get the word out so we can build up a base here.

AMI Webinar: connecting, inspiring and advocating for LGBTQIA+ researchers in microbiology

Calling all queer microbiologists 🏳️‍🌈🦠🧫

Applied Microbiology International are hosting a webinar TODAY 3pm-4.30pm GMT. It’s free.

Delighted to be one of the panel members for this event 😁

appliedmicrobiology.org/ems-event-ca...

#queerinmicro #queerinstem

Illustration of people falling of a cliff edge made of antibiotic pills. Overlad with text: "News - Using AI to treat infections more accurately"

New research led by ISMIB's Dr Alex Howard & @camo-net.bsky.social shows how artificial intelligence can predict antibiotic resistance in UTIs, helping personalise treatment options and tackle #AMR.

#NatureCommunications #WAAW24 #AI

news.liverpool.ac.uk/2024/11/21/u...

Fabulous post sharing thoughts on proteomics technologies - bang on @rdunwin.bsky.social !!

PhosX is out! doi.org/10.1093/bioi... Leveraging the latest kinase specificity maps by the Cantley, Yaffe, and Turk labs and a rank sum statistic we created PhosX so now we can predict activities for nearly all kinases in your phosphodata, including the understudied ones. Check it out!

Major funding to support next generation of bioscience researchers

Great news! In partnership with the University of Manchester, we have been awarded a major new Doctoral Landscape Award from the BBSRC to fund #PhD training in the #biosciences. 🌱🔬

Read more about the new NorthWest Doctoral Programme in Biosciences (NWD) ▶️ news.liverpool.ac.uk/2024/11/20/u...

My 2 c - It can be very helpful for editors if there is information detailing the relevant expertise of those suggestions to give more choice, but ultimately the risk relates to the integrity of the handling editor potentially just accepting the opinion of the authors 'friends'

YouTube video by The Pandemic Institute Pandemic Preparedness - Purpose & Data Driven Testing

A short film to thank the people of #Liverpool for showing the way forward in #COVID19 community testing in November 2020, and a framework for future pandemic testing preparedness from a series of expert panels for #UKHSA #DataSavesLives #PublicHealth youtu.be/60Z6c0V_VKg

It's exciting getting to catch up with friends again, but it might take me a while to get set up. In the meantime here's a puppy picture to put a smile on your Saturday

Veneer is a tool to standardize and improve how cell surface proteomics data are interpreted and distributed. Also highlights sequon frequencies in data for flagging potentially problematic datasets.

pubs.acs.org/doi/10.1021/...