A systematic approach to the analysis of protein phosphorylation

• Published in: Nature biotechnology 2001-04, Vol.19 (4), p.375-378
• Main Authors: Zhou, Huilin, Watts, Julian D., Aebersold, Ruedi
• Format: Article
• Language: English
• Subjects: Acids; Agriculture; Amino Acid Sequence; Biochemistry - methods; Bioinformatics; Biological and medical sciences; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Caseins - chemistry; Chemical reactions; Databases, Factual; Diverse techniques; Fundamental and applied biological sciences. Psychology; Fungal Proteins - chemistry; Gas Chromatography-Mass Spectrometry - methods; Glucose - chemistry; Glutathione Transferase - metabolism; Homogeneity; Kinases; Life Sciences; Liquid chromatography; Mass spectrometry; Mass Spectrometry - methods; Models, Chemical; Molecular and cellular biology; Molecular Sequence Data; Peptides; Peptides - chemistry; Peptides - isolation & purification; Phosphorylation; Proteins; Recombinant Fusion Proteins - metabolism; Saccharomyces cerevisiae - enzymology; Serine - chemistry; technical-report; Threonine - chemistry; Time Factors; Tyrosine - chemistry; Yeasts
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/86777

Reversible protein phosphorylation has been known for some time to control a wide range of biological functions and activities 1 , 2 , 3 . Thus determination of the site(s) of protein phosphorylation has been an essential step in the analysis of the control of many biological systems. However, direct determination of individual phosphorylation sites occurring on phosphoproteins in vivo has been difficult to date, typically requiring the purification to homogeneity of the phosphoprotein of interest before analysis 4 , 5 , 6 . Thus, there has been a substantial need for a more rapid and general method for the analysis of protein phosphorylation in complex protein mixtures. Here we describe such an approach to protein phosphorylation analysis. It consists of three steps: (1) selective phosphopeptide isolation from a peptide mixture via a sequence of chemical reactions, (2) phosphopeptide analysis by automated liquid chromatography–tandem mass spectrometry (LC-MS/MS), and (3) identification of the phosphoprotein and the phosphorylated residue(s) by correlation of tandem mass spectrometric data with sequence databases. By utilizing various phosphoprotein standards and a whole yeast cell lysate, we demonstrate that the method is equally applicable to serine-, threonine- and tyrosine-phosphorylated proteins, and is capable of selectively isolating and identifying phosphopeptides present in a highly complex peptide mixture.