Data Independent Acquisition (DIA) Profiling
DIA is now our Default for Quantitative proteomic profiling. It's much better than our older Label free methods we have used in teh past and is much cheaper and faster than TMT (see below)
- Can be very inexpensive (< 50 / sample)
- Good proteome Depth!
- Sensitive (down to single cell level is possible)
- Fast Turn around time if you do the sample prep
- Data analysis can be easier than other methods
- Does not work well for some esoteric PTM's
- Sometimes does not work well for very complex multispecies proteomes
For More info see this presentation
Why We use DIA at the UC Davis Proteomics Core
Some of our recent Example Publications
Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes Published in Cell
Proximity proteomics of C9orf72 dipeptide repeat proteins identifies molecular chaperones as modifiers of poly-GA aggregation
Stress granules and mTOR are regulated by membrane atg8ylation during lysosomal damage
Interactomic analysis reveals a homeostatic role for the HIV restriction factor TRIM5α in mitophagy
Still generates really good data!
- Good quantitative Data
- Good proteome Depth with peptide Fractionation
- Optimally should be analyzed on our most expensive mass spectrometer
- Turn around time is long if you want us to do the labeling
TMT is a reporter ion isotope labeled balanced set of tag’s (currently 18) .
- digest proteins into peptides,
- label with TMT, which labels free amines (K and N-term)
- Mix your samples together (create a multiplex)
- Fractionate your samples using high pH fractionation if your sample is very complex (lysate for example)
- Analyze your peptide fractions using SPS MS3 on our Fusion Lumos
Some of our Example Publications
De Novo Arginine Synthesis Is Required for Full Virulence of Xanthomonas arboricola pv. juglandis During Walnut Bacterial Blight Disease
A Secreted Chorismate Mutase from Xanthomonas arboricola pv. juglandis Attenuates Virulence and Walnut Blight Symptoms
Proteome analysis of walnut bacterial blight disease
Gender-specific changes in energy metabolism and protein degradation as major pathways affected in livers of mice treated with ibuprofen
Here is a presentation of a dataset we did recently. The author of the above publication helps us with the analysis. Make sure you read the notes as most of the detailed info is located there.