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
Proteomics
TMT goes 11-plex!

Thermo Fisher releases TMT 11-plex. Thermo Fisher recently released an additional channel for TMT, which means you can now combine up to 11 different samples as one for better sample comparability and more complete data! It is now possible to use “isotopologue” encoding to split the 131 (last) channel into 131-N and 131-C to get […]

News
ADAPTED Project Press Release

New project to explore overlooked area of Alzheimer’s Disease research Alzheimer’s disease (AD) affects over 35 million people world-wide at present, these numbers are expected to grow substantially over the next few decades and there are currently no medicines which slow the progress of the disease. To boost the development of new medicines for AD, […]

Dr. Francesco Rao
Proteomics
Database Searching

Ideally, each MS2 spectrum would contain enough information to go back unambiguously to the sequence of its parent precursor. Since this is actually rarely the case, a strategy called Database Searching is usually used instead. MS2 fragmentation spectra are used to identify the sequence behind their MS1 parent peak. However, MS2 spectra rarely allow unambiguous […]

Dr. Armel Nicolas
Point of View