I want to quantify certain proteins using label free peptide peak intensity based method; for this I feel first of all I should know the retention time of identified peptides, and after identifying RT only I can go for quantification of peptides.
I am not very sure of my approach but I feel this is doable and many should be doing this on regular basis. Please can any one explain how can I identify RT of my peptides in my Ab Sciex 5600 Triple TOF system where I have run the sample only for the identification of proteins from a given cell lysate .
If you have some better strategies to quantify proteins using label free methods, please suggest me that as well, I am open for that as well.
In advance Big Thanks :)
Hi Joel,
MaxQuant is the best software that is publicly available (free) and that can quantitate intensity and retention time based quantitation of peptides:
http://www.nature.com/nprot/journal/v4/n5/full/nprot.2009.36.html
Good luck.
Hediye
Hi Joel,
I would also suggest you take a look at Skyline, the software is excellent and works with a range of identification programs (Mascot, X!Tandem, MS-GF+ etc).
Whilst MaxQuant is good software, it was originally developed for Thermo data. It is now supposed to work with 5600 data, but I have colleagues that have had less than spectacular results when they used it recently. Things may have changed, so it's worth investigating, but don't be surprised if it doesn't meet expectations.
There are numerous other free and commercial software that do MS1 quant, or spectral counting. Ask Google...
Enjoy,
Peter
https://skyline.gs.washington.edu/labkey/project/home/begin.view?
Thanks Peter. You are right; my experience with MaxQuant has been with Thermo data and I am not sure how MaxQuant behaves with Sciex data.
Skyline works well with Sciex MRM kind of data so Joel, your first choice should probably be to use Skyline.
Best,
Hediye.
Thank you very much for valuable answers, I am already using skyline to generate MRM transitions but I was unaware about its use to identify RT and intensity of peptides.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides