Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹⁸O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography

Journal Article · Wed Oct 01 00:00:00 EDT 2008 · Journal of Proteome Research, 7(10):4215-24

DOI:https://doi.org/10.1021/pr7007785· OSTI ID:974991

Ding, Shi-Jian; Wang, Yingchun; Jacobs, Jon M; Qian, Weijun; Yang, Feng; Tolmachev, Aleksey V; Du, Xiuxia; Wang, Wei; Moore, Ronald J; Monroe, Matthew E; Purvine, Samuel O; Waters, Katrina M; Heibeck, Tyler H; Adkins, Joshua N; Camp, David G; Klemke, Richard L; Smith, Richard D

Reversible protein phosphorylation is a central cellular regulatory mechanism in modulating protein activity and propagating signals within cellular pathways and networks. Development of more effective methods for the simultaneous identification of phosphorylation sites and quantification of temporal changes in protein phosphorylation could provide important insights into molecular signaling mechanisms in a variety of different cellular processes. Here we present an integrated quantitative phosphoproteomics approach and its applications for comparative analysis of Cos-7 cells in response to lysophosphatidic acid (LPA) gradient stimulation. The approach combines trypsin-catalyzed 16O/18O labeling plus 16O/18O-methanol esterification labeling for quantitation, a macro- Immobilized Metal-ion Affinity Chromatography trap for phosphopeptide enrichment, and a monolithic capillary column with integrated electrospray emitter. LC separation and MS/MS is followed by neutral loss-dependent MS/MS/MS for phosphopeptide identification using a linear ion trap (LTQ)-FT mass spectrometer and complementary searching algorithms for interpreting MS/MS spectra. Protein phosphorylation involved in various signaling pathways of cell migration were identified and quantified, such as mitogen-activated protein kinase 1, dual-specificity mitogen-activated protein kinase kinase 2, and dual-specificity tyrosine-phosphorylation regulated kinase 1b, and a number of Rho GTPase-activating proteins. These results demonstrate the efficiency of this quantitative phosphoproteomics approach and its application for rapid discovery of phosphorylation events associated with gradient sensing and cell chemotaxis.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 974991
• Report Number(s): PNNL-SA-52241; 24698; 400412000; TRN: US201007%%930
• Journal Information: Journal of Proteome Research, 7(10):4215-24, Vol. 7, Issue 10
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
AFFINITY
ALGORITHMS
CHROMATOGRAPHY
EFFICIENCY
ESTERIFICATION
MASS SPECTROMETERS
PHOSPHORYLATION
PHOSPHOTRANSFERASES
PROTEINS
SPECTRA
STIMULATION
LTQ
linear ion trap
SIM
selected ion monitoring
LC-MS: liquid chromatography coupled with mass spectrometry
PTMs
post-translational modifications
pSer
phosphoserine
pThr
phosphothreonine
pTyr
phosphotyrosine
IMAC
immobilized metal-ion affinity chromatography
LPA
lysophosphatidic acid
Erk2
mitogen-activated protein kinase 1
CDK1: Cell Division Cycle 2 Protein Isoform 2
Environmental Molecular Sciences Laboratory