title: Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry.
abstract: While human plasma serves as a great source for disease diagnosis, low-molecular-weight (LMW) proteome (<30 kDa) has been shown to contain a rich source of diagnostic biomarkers. Here we employ top-down mass spectrometry to analyze the LMW proteoforms present in four types of human plasma samples pooled from three healthy controls (HCs) without immunoaffinity depletion and with depletion of the top two, six, and seven high-abundance proteins. The LMW proteoforms were first fractionated based on molecular weight using gel-eluted liquid fraction entrapment electrophoresis (GELFrEE). Then, the GELFrEE fractions containing up to 30 kDa were subjected to nanocapillary-LC-MS/MS, and the high-resolution MS and MS/MS data were processed using ProSightPC 3.0. As a result, a total of 442 LMW proteins and cleaved products, including those with post-translational modifications and single amino acid variations, were identified. From additional comparative analysis of plasma samples without immunoaffinity depletion between HCs and colorectal cancer (CRC) patients via top-down approach, tens of LMW proteoforms, including platelet factor 4, were found to show >1.5-fold changes between the plasma samples of HCs and CRC patients, and six of the LMW proteins were verified by Western blot analysis.
authors.affiliation: Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Republic of Korea.|Interdisciplinary Program of Integrated Biotechnology, Sogang University , Seoul 121-742, Republic of Korea.
authors.forename: Dong Huey
authors.initials: DH
authors.lastname: Cheon
authors.affiliation: Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Republic of Korea.|Department of Chemistry, Kyungpook National University , Daegu 702-701, Republic of Korea.
authors.forename: Eun Ji
authors.initials: EJ
authors.lastname: Nam
authors.affiliation: Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital , Seongnam 463-707, Republic of Korea.
authors.forename: Kyu Hyung
authors.initials: KH
authors.lastname: Park
authors.affiliation: Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital , Seongnam 463-707, Republic of Korea.
authors.forename: Se Joon
authors.initials: SJ
authors.lastname: Woo
authors.affiliation: Department of Chemistry, Kyungpook National University , Daegu 702-701, Republic of Korea.
authors.forename: Hye Jin
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 135-710, Republic of Korea.
authors.forename: Hee Cheol
authors.initials: HC
authors.lastname: Kim
authors.affiliation: Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Republic of Korea.
authors.forename: Eun Gyeong
authors.initials: EG
authors.lastname: Yang
authors.affiliation: Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Republic of Korea.|Department of Biological Chemistry, University of Science and Technology , Daejeon 305-333, Republic of Korea.
authors.forename: Cheolju
authors.initials: C
authors.lastname: Lee
authors.affiliation: Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Republic of Korea.
authors.forename: Ji Eun
authors.initials: JE
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D014408:Biomarkers, Tumor / Q000097:blood* / Q000737:chemistry / Q000302:isolation & purification; D001798:Blood Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D016022:Case-Control Studies; D056148:Chromatography, Reverse-Phase; D015179:Colorectal Neoplasms / Q000097:blood* / Q000175:diagnosis; D006801:Humans; D008969:Molecular Sequence Data; D008970:Molecular Weight; D053719:Tandem Mass Spectrometry
chemical_list: D014408:Biomarkers, Tumor; D001798:Blood Proteins
keywords: biomarker; cleaved products; colorectal cancer (CRC); gel-eluted liquid fraction entrapment electrophoresis (GELFrEE); human plasma; low-molecular-weight (LMW) plasma proteins; post-translational modification (PTM); single amino acid variation (SAAV); top-down mass spectrometry