title: Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform-independent separation.
abstract: CE-MS is a successful proteomic platform for the definition of biomarkers in different body fluids. Besides the biomarker defining experimental parameters, CE migration time and molecular weight, especially biomarker's sequence identity is an indispensable cornerstone for deeper insights into the pathophysiological pathways of diseases or for made-to-measure therapeutic drug design. Therefore, this report presents a detailed discussion of different peptide sequencing platforms consisting of high performance separation method either coupled on-line or off-line to different MS/MS devices, such as MALDI-TOF-TOF, ESI-IT, ESI-QTOF and Fourier transform ion cyclotron resonance, for sequencing indicative peptides. This comparison demonstrates the unique feature of CE-MS technology to serve as a reliable basis for the assignment of peptide sequence data obtained using different separation MS/MS methods to the biomarker defining parameters, CE migration time and molecular weight. Discovery of potential biomarkers by CE-MS enables sequence analysis via MS/MS with platform-independent sample separation. This is due to the fact that the number of basic and neutral polar amino acids of biomarkers sequences distinctly correlates with their CE-MS migration time/molecular weight coordinates. This uniqueness facilitates the independent entry of different sequencing platforms for peptide sequencing of CE-MS-defined biomarkers from highly complex mixtures.
authors.affiliation: Mosaiques Diagnostics & Therapeutics AG, Hannover, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Zürbig
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Renfrow
authors.forename: Eric
authors.initials: E
authors.lastname: Schiffer
authors.forename: Jan
authors.initials: J
authors.lastname: Novak
authors.forename: Michael
authors.initials: M
authors.lastname: Walden
authors.forename: Stefan
authors.initials: S
authors.lastname: Wittke
authors.forename: Ingo
authors.initials: I
authors.lastname: Just
authors.forename: Matthias
authors.initials: M
authors.lastname: Pelzing
authors.forename: Christian
authors.initials: C
authors.lastname: Neusüss
authors.forename: Dan
authors.initials: D
authors.lastname: Theodorescu
authors.forename: Karen E
authors.initials: KE
authors.lastname: Root
authors.forename: Mark M
authors.initials: MM
authors.lastname: Ross
authors.forename: Harald
authors.initials: H
authors.lastname: Mischak
mesh_terms: D000595:Amino Acid Sequence; D015415:Biomarkers / Q000032:analysis* / Q000097:blood / Q000652:urine; D001826:Body Fluids / Q000737:chemistry; D019075:Electrophoresis, Capillary / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D009862:Online Systems; D010455:Peptides / Q000032:analysis; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
chemical_list: D015415:Biomarkers; D010455:Peptides