Facility: DDA vs DIA
Introduction For many years proteomics type mass spec experiments were all acquired using the same basic approach, Data Directed Analysis (DDA), but now a new acquisition methodology is becoming more popular Data Independant Analysis (DIA). In this post I’ll describe...
Facility: Investigating protein purity
Investigating protein purity is a tricky though valuable question. The reason why it is tricky is that there are many different ways at looking at a biological sample to see what may have gone wrong e.g... Have my proteins been post-translationally modified (e.g....
User Story: Understanding the proteomic signature of the zebrafish embryonic kidney (the pronephros)
Understanding the proteomic signature of the zebrafish embryonic kidney (the pronephros)Name: Richard NaylorPosition when you did the work: Postdoc (RA)Who’s lab were you in: Lennon laboratoryWhat was the biology you were studying:I wished to identify the proteomic...
Facility: Mass spec matchups – QE HF vs Orbitrap Elite
IntroductionMatch-UP posts compares mass spec systems in the BioMS facility to give you an idea of how they compare. They are fact based but there will also be chunks of opinion and experience as well so these comparisons should be considered the beginnings of...
Basics: Understanding LC-MS technologies
IntroductionThis post is to help you understand the technologies involved in LC-MS systems. LC-MS systems contain or are configured with mixtures of different types of technologies that give each a different capability. Understanding the different technologies helps...
Facility: Sample submission guidelines
Active fromFebruary 2020Introduction:The BioMS Facility is there to help you obtain the best possible data in a timely fashion. To do this the facility needs to have all the relevant information to ensure the correct analyses are performed and to know where your...
Methods: Covaris disruption of protein samples before S-Trap sample preparation
OverviewThe purpose of this method is to effectively disrupt samples to solubilse proteins ready for clean-up and digestion before mass spec analysis. The benefits of using the Covaris systems are as follows:High energy disruption to ensure physical structures are...
Workflow: Covaris> S-Trap> R3> QE> ProteomeDiscoverer
OverviewThis workflow is preparing global proteomics samples in a generic easy to use way. It uses focussed ultrasonication in the Covaris systems in the facility using highly aggressive buffers and this approach has been demonstrated to work with every sample type...
Introduction: Proteomics
Overview Proteomics is the quantitative study of the total expressed protein within a biological environment. This is traditionally within a cell or tissue but it can also be used in other environments such as cell media or enrichments of specific sub families of...
Lab methodolgies: Gel-tops
Gel-top analysis is a method of preparing samples for in-gel digestion. The aim is to trap your entire sample in a small section of polyacrylamide gel for analysis as a single sample. We do not have a fixed protocol for preparing samples for 'gel-top' analysis but...
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