Deep proteomic profiling of human carotid atherosclerotic plaques using multidimensional LC-MS/MS.
OBJECTIVE
To increase the proteome coverage of human atherosclerotic plaques and identify low-abundance proteins that may have important functions during the development and progression of atherosclerosis.


METHODS
Thirty-eight human carotid atherosclerotic plaques were pooled into two samples and analyzed in triplicate using offline multidimensional LC-MS/MS. The collected fractions of trypsin-digested peptides from Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) were analyzed by LC-MS/MS on a Q Exactive (Thermo Fisher, MA, USA).


RESULTS
A total of 4702 proteins were identified from atherosclerotic plaques at a false discovery rate (FDR) of 1%, of which 3846 were identified with at least 2 unique peptides. Many pathways related to the development and progression of atherosclerosis were identified, such as atherosclerosis signaling, toll receptor signaling pathway and inhibition of matrix metalloproteases. Many low-abundance proteins with important functions in atherosclerosis that were previously unidentifiable using mass spectrometry based proteomics methods, such as TGF-β, interleukins and other growth factors, were identified confidently from plaques.


CONCLUSIONS
This study has substantially increased the coverage of the atherosclerotic plaque proteome which represents a leap forward in understanding of plaque composition, development and progression. The identification of many low-abundance proteins may also facilitate biomarker discovery.
School of Biological Sciences, Nanyang Technological University, Singapore; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
Piliang
P
Hao
Yan
Y
Ren
Gerard
G
Pasterkamp
Frans L
FL
Moll
Dominique P V
DP
de Kleijn
Siu Kwan
SK
Sze
D000368:Aged; D000369:Aged, 80 and over; D002340:Carotid Artery Diseases / Q000378:metabolism*; D002853:Chromatography, Liquid; D018450:Disease Progression; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D058226:Plaque, Atherosclerotic / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
Atherosclerotic plaques; Biomarkers; Carotid arteries