Class notes
Proteomics and biomedical applications
- Course
- Institution
Lecture notes on Proteomics and biomedical applications
[Show more]
Seller
Follow
polinalobacheva
Reviews received
Content preview
What is proteomics?- The global / large scale study of proteins
- Comparable to DNA for genomics
- Big difference: unlike DNA, amplification of proteins is not possible
- The term proteome was first used in 1997
- The proteome is the entire set of proteins produced or modified by an organism or system
- While proteomics generally refers to the large-scale experimental analysis of proteins, it is often specifically used
for mass spectrometry applications with or without protein purification
- The field is full of acronyms!
- SILAC, iTRAQ, ESI, MALDI, TOF, TMT, SRM, MS1, MS2 etc
- Importantly it can be used to not just define the components of systems but to quantify them
The mass-spectrometry (MS) /proteomic experiment:
- An experiment comprises many steps coupled together. Sample preparation, enzymatic digestion,
chromatography, ionisation, MS, informatics (not just database matching)
- All steps are critical to the successful outcome of the experiment
- A variety of quantitative workflows are available
- No standardised method agreed
- A proteomics workflow does not stop when you have a list of peptides / proteins
- Informatic analysis required e.g. statistics for abundance / volcano plots / pathway analysis / principal component
analysis (PCA) / hierarchical clustering / protein-protein interaction networks
, The liquid-chromatography (LC) –tandem mass
spectrometry (MSMS) experiment
Liquid-Chromatography (LC) is a method that is
coupled inline to allow separation of peptides before
ionisation
- MALDI – Matrix Assisted Laser Desorption
Ionisation - Lower throughput
- ESI – ElectroSpray Ionisation - Higher throughput
- most popular method
- HPLC – High-Performance (High-Pressure) Liquid
Chromatography
MS measures mass to charge ratios (m/z) (of
peptides)
Peptide sequencing and database matching
- Peptides are selected in the MS for
fragmentation
- Peptides fragment at the peptide bond in a
characteristic way
- Terminology for ions is abc and xyz
- Fragmentation at various positions along the
peptide backbone generates fragments of
different lengths
- The peaks seen are a sum of many copies of the
selected molecule snapping in different places
- Matching MS spectra to a database is a
probability-based exercise
Approaches of quantitative proteomics:
Relative or absolute quantification?
The benefits of buying summaries with Stuvia:
Guaranteed quality through customer reviews
Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.
Quick and easy check-out
You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.
Focus on what matters
Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!
Frequently asked questions
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
Satisfaction guarantee: how does it work?
Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.
Who am I buying these notes from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller polinalobacheva. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy these notes for $13.00. You're not tied to anything after your purchase.
Can Stuvia be trusted?
4.6 stars on Google & Trustpilot (+1000 reviews)
75759 documents were sold in the last 30 days
Founded in 2010, the go-to place to buy study notes for 14 years now