Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics.

@article{Dwivedi2008PracticalIO,
  title={Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics.},
  author={Ravi Chandra Dwivedi and Vic Spicer and Michael Harder and Mihaela Antonovici and Werner E Ens and Kenneth G Standing and John A. Wilkins and Oleg V Krokhin},
  journal={Analytical chemistry},
  year={2008},
  volume={80 18},
  pages={7036-42}
}
We describe the practical implementation of a new RP (pH 10 - pH 2) 2D HPLC-ESI/MS scheme for large-scale bottom-up analysis in proteomics. When compared to the common SCX-RP approach, it provides a higher separation efficiency in the first dimension and increases the number of identified peptides/proteins. We also employed the methodology of our sequence-specific retention calculator (SSRCalc) and developed peptide retention prediction algorithms for both LC dimensions. A diverse set of… CONTINUE READING

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