Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.
Targeted quantitative proteomics by mass spectrometry aims to selectively detect one or a panel of peptides/proteins in a complex sample and is particularly appealing for novel biomarker verification/validation because it does not require specific antibodies. Here, we demonstrated the application of targeted quantitative proteomics in searching, identifying, and quantifying selected peptides in human cerebrospinal spinal fluid (CSF) using a matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF)-based platform. The approach involved two major components: the use of isotopic-labeled synthetic peptides as references for targeted identification and quantification and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The platform provides high confidence for targeted peptide detection in a complex system and can potentially be developed into a high-throughput system. Using the liquid chromatography (LC) MALDI TOF/TOF platform and the complementary identification strategy, we were able to selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins. The effectiveness and robustness of the approach associated with different sample complexity, sample preparation strategies, as well as mass spectrometric quantification were evaluated. Other issues related to chromatography separation and the feasibility for high-throughput analysis were also discussed. Finally, we applied targeted quantitative proteomics to analyze a subset of previously identified candidate markers in CSF samples of patients with Parkinson's disease (PD) at different stages and Alzheimer's disease (AD) along with normal controls.
Pan
Sheng
S
Department of Pathology, University of Washington, Seattle, Washington 98195, USA. span@u.washington.edu
Rush
John
J
Peskind
Elaine R
ER
Galasko
Douglas
D
Chung
Kathryn
K
Quinn
Joseph
J
Jankovic
Joseph
J
Leverenz
James B
JB
Zabetian
Cyrus
C
Pan
Catherine
C
Wang
Yan
Y
Oh
Jung Hun
JH
Gao
Jean
J
Zhang
Jianpeng
J
Montine
Thomas
T
Zhang
Jing
J
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000595:Amino Acid Sequence; D002556:Cerebrospinal Fluid Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D019636:Neurodegenerative Diseases / Q000134:cerebrospinal fluid; D040901:Proteomics; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000295:instrumentation / Q000379:methods*
D002556:Cerebrospinal Fluid Proteins