An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion

摘要

Aberrant protein phosphorylation plays important roles in cancer-related cell signaling. Towards multiplexed, comprehensive and fully automatic for quantitative phosphoproteomics, we present a simple label-free strategy combining automatic pH/acid controlled IMAC procedure and SEMI (Sequence, Elution time, Mass to charge and Internal standard) assisted algorithm. The high quantitation accuracy and precision can be obtained by our reproducible IMAC protocol and the internal standard can minimize system variation. Most importantly, the SEMI algorithm performs chromatographic alignment based on confidently identified peptides followed by peptide cross-assignment in all LC-MS/MS runs, thus increasing the number of quantifiable peptides. This approach was demonstrated on the first delineation of quantitative phosphoproteomics profiles of lung cancer metastasis model to explore the metastasis-associated phosphoproteomic alteration in lung cancer.