Comparison of Label-free Proteome Quantification Methods on Standards and Retinoic Acid Treated Cells

摘要

Spectral Counting: Pros: fast data processing, high sensitivity. Cons: large percent error, whole number output (minimizes accuracy). PICA: Pros: high accuracy, high sensitivity. Cons: slow data processing, command line intensive. SIEVE: Pros: fast data processing, "point and click" interface. Cons: low sensitivity, limited application (difficulty with gas-phase fractionation). Application: Label-free quantification of RA proteome identifies known proteins involved in RA-mediated apoptosis and cell cycle regulation. Uncovered novel protein pathways regulated by exposure to RA. Effective, high-throughput method for differential proteome analysis applicable to all sample types.