Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.
Despite recent advances in instrumentation and analytical strategies for identification and quantitation of protein phosphorylation, a highly specific enrichment protocol is still a challenge in large-scale studies. Here, we report a simple pH/acid control method that addresses the poor specificity seriously criticized in IMAC. Detailed evaluation of the capture and release mechanism in IMAC revealed that pH, buffer and salt yield a complex interplay in enrichment of phosphopeptides, yet they play individual roles in recovery and specificity. A revised one-step IMAC method with low sample loss and high specificity can be rationally designed by controlling salt, pH and the structure and concentration of organic acid. Without methyl esterification, the one-step IMAC enrichment with single LC-MS/MS identified 386 phosphoproteins in 550 mug of non-small-cell lung cancer cell lysate with 96% specificity. Additional fractionation by SDS-PAGE from 4 mg of cell lysate revealed the comprehensive proteome map, identifying 2747 phosphorylation sites from 2360 nondegenerate phosphopeptides and 1219 phosphoproteins with a false discovery rate of 0.63%. To our knowledge, this pH/acid-controlled IMAC procedure provides higher specificity than any other one-step IMAC purification procedure. Furthermore, the simple and reproducible IMAC protocol can be adapted to other solid supports, fully automated or manual, for large-scale identification of the vastly under-explored phosphoproteome.
Tsai
Chia-Feng
CF
Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan.
Wang
Yi-Ting
YT
Chen
Yet-Ran
YR
Lai
Chen-Yu
CY
Lin
Pei-Yi
PY
Pan
Kuan-Ting
KT
Chen
Jeou-Yuan
JY
Khoo
Kay-Hooi
KH
Chen
Yu-Ju
YJ
D000143:Acids / Q000737:chemistry*; D045744:Cell Line, Tumor; D002846:Chromatography, Affinity / Q000379:methods*; D030562:Databases, Protein; D004591:Electrophoresis, Polyacrylamide Gel; D006801:Humans; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D008670:Metals / Q000737:chemistry*; D010750:Phosphoproteins / Q000737:chemistry*; D020543:Proteome; D053719:Tandem Mass Spectrometry
D000143:Acids; D008670:Metals; D010750:Phosphoproteins; D020543:Proteome