News
When will you Click?

Click chemistry reactions are reactions between an alkyne-tagged molecule and an azide-tagged molecule which use copper as a catalyst. This was introduced by K. B. Sharpless in 2001 for which he was awarded half of the 2001 Nobel Prize in Chemistry. Sharpless developed these reactions in The Scripps Institute, California and has continued developing more […]

Shona Patton
Proteomics
Where to draw the line? Hypothesis Testing in Proteomics

So, you’ve got this beautiful proteomics experiment done. You just got your data (yay!), let’s say ratios of treated vs control, 3 replicates, simple experiment. But that’s thousands of protein groups, most of which are probably not interesting at all. We want to find out which proteins are regulated. How do we do it?   […]

Dr. Armel Nicolas
Proteomics
ADAPTED Project meeting in Edinburgh – understanding APOE

This week Francesco Rao attended a progress meeting for the ADAPTED project. For this meet up the city of choice was Edinburgh, some might argue the most beautiful city in the world! After a successful launch year, this was the first consortium meeting in 2018. With someone in the world developing Dementia every 3 seconds, the […]

Sarah Macdonald
Proteomics
Through the Looking Glass: Peptide identification

In previous instalments, we looked at what happens to the poor peptides we send to their doom down the rabbit hole and into the strange wonderland that is the inside of a mass spectrometer[1]. Now, it’s all fine and good to fragment peptides into tiny little pieces, I for one am all for it. I […]

Armel Nicolas
Proteomics
Follow The White Rabbit – Interpreting Individual Peaks – MS2 spectra

Hi everyone, and welcome to a glorious New Year! 2017 was fun, wasn’t it? I for one so much look forward to 2018 being slightly more normal. Oh what the hell, who am I kidding, I’ll get some popcorn already. Today, we will be talking about MS2 spectra, that is, the spectra resulting from the […]

Armel Nicolas
Proteomics
Down The Rabbit Hole: what does a peptide look like in MS?

Interpreting Individual Peaks – part 1 If you have ever looked at a mass-spectrometer output file, you may have wondered how it is possible to make sense of all of these peaks. I mean, there really is a lot of them! Here, we will talk a bit about the basic rules which govern the behaviour […]

Armel Nicolas
Proteomics
What a tangled web we unweave – deciphering raw proteomics data

Today we will be speaking of proteomics data files and their contents. We will also talk a bit about proteomics file formats, and why they are a mess. In a typical case, you would have been running peptide samples on a mass-spectrometer using a gradient to separate peptides by some physicochemical property so they don’t […]

Armel Nicolas
Proteomics
Making Sense of LC-MS/MS Spectra – Part I

From lots of gibberish to useful data… This post is destined to become the introduction of a new series of glorious blog entries on the subject of LC-MS/MS data analysis.   In this series we would like to talk about proteomics data analysis and the different steps it involves. The series will focus on the […]

Armel Nicolas
News
ADAPTED Project meeting in Bonn – tackling Alzheimer’s Disease

Last week, my colleague Francesco Rao (DC Biosciences’ CSO) and I travelled to Bonn to participate in a progress meeting for ADAPTED (Alzheimer’s Disease Apolipoprotein Pathology for Treatment Elucidation and Development).     Bonn, the birthplace of Beethoven (though everyone’s favourite tortured pre-romantic composer spent most of his years in Vienna), is a relatively small city […]

Dr. Armel Nicolas
Proteomics
Is this the future of LC-MS/MS?

Mass spectrometry-based proteomics is an amazing and still fast evolving field. The way clever people constantly come up with new ways to tweak experiment design to tackle wholly different biological questions never ceases to amaze me. When I started in MS, I had mostly heard of people using MALDI-TOF instruments. Orbitraps were just emerging as […]

Dr. Armel Nicolas
Point of View