title: Sequencing and quantifying IgG fragments and antigen-binding regions by mass spectrometry.
abstract: In cancer and autoimmune diseases, immunoglobulins with a specific molecular signature that could potentially be used as diagnostic or prognostic markers are released into body fluids. An immunomics approach based on this phenomenon relies on the ability to identify the specific amino acid sequences of the complementarity-determining regions (CDR) of these immunoglobulins, which in turn depends on the level of accuracy, resolution, and sensitivity that can be achieved by advanced mass spectrometry. Reproducible isolation and sequencing of antibody fragments (e.g., Fab) by high-resolution mass spectrometry (MS) from seven healthy donors revealed 43 217 MS signals: 225 could be associated with CDR1 peptides, 513 with CDR2 peptides, and 19 with CDR3 peptides. Seventeen percent of the 43 217 MS signals did not overlap between the seven donors. The Fab isolation method used is reproducible and fast, with a high yield. It provides only one Fab sample fraction for subsequent characterization by high-resolution MS. In 17% and 4% of these seven healthy donors, qualitative (presence/absence) and quantitative (intensity) differences in Fab fragments could be demonstrated, respectively. From these results, we conclude that the identification of a CDR signature as biomarker for autoimmune diseases and cancer without prior knowledge of the antigen is feasible.
authors.affiliation: Department of Pulmonology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Dominique
authors.initials: D
authors.lastname: de Costa
authors.forename: Ingrid
authors.initials: I
authors.lastname: Broodman
authors.forename: Martijn M
authors.initials: MM
authors.lastname: Vanduijn
authors.forename: Christoph
authors.initials: C
authors.lastname: Stingl
authors.forename: Lennard J M
authors.initials: LJ
authors.lastname: Dekker
authors.forename: Peter C
authors.initials: PC
authors.lastname: Burgers
authors.forename: Henk C
authors.initials: HC
authors.lastname: Hoogsteden
authors.forename: Peter A E
authors.initials: PA
authors.lastname: Sillevis Smitt
authors.forename: Rob J
authors.initials: RJ
authors.lastname: van Klaveren
authors.forename: Theo M
authors.initials: TM
authors.lastname: Luider
mesh_terms: D000368:Aged; D000595:Amino Acid Sequence; D000704:Analysis of Variance; D022801:Complementarity Determining Regions / Q000737:chemistry*; D005260:Female; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000097:blood* / Q000737:chemistry / Q000378:metabolism; D007074:Immunoglobulin G / Q000097:blood* / Q000737:chemistry / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D016415:Sequence Alignment; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D022801:Complementarity Determining Regions; D007140:Immunoglobulin Fab Fragments; D007074:Immunoglobulin G