title: 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.
abstract: 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.
authors.affiliation: Department of Pathology, University of Washington, Seattle, Washington 98195, USA. span@u.washington.edu
authors.forename: Sheng
authors.initials: S
authors.lastname: Pan
authors.forename: John
authors.initials: J
authors.lastname: Rush
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Peskind
authors.forename: Douglas
authors.initials: D
authors.lastname: Galasko
authors.forename: Kathryn
authors.initials: K
authors.lastname: Chung
authors.forename: Joseph
authors.initials: J
authors.lastname: Quinn
authors.forename: Joseph
authors.initials: J
authors.lastname: Jankovic
authors.forename: James B
authors.initials: JB
authors.lastname: Leverenz
authors.forename: Cyrus
authors.initials: C
authors.lastname: Zabetian
authors.forename: Catherine
authors.initials: C
authors.lastname: Pan
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Jung Hun
authors.initials: JH
authors.lastname: Oh
authors.forename: Jean
authors.initials: J
authors.lastname: Gao
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Zhang
authors.forename: Thomas
authors.initials: T
authors.lastname: Montine
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
mesh_terms: 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*
chemical_list: D002556:Cerebrospinal Fluid Proteins