De novo sequencing of antibody light chain proteoforms from patients with multiple myeloma

ABSTRACT: In multiple myeloma diseases, monoclonal immunoglobulin light chains (LCs) are abundantly produced, with as a consequence in some cases the formation of deposits affecting various organs, such as kidney, while in other cases to remain soluble up to concentrations of several g.L-1 in plasma. The exact factors crucial for the solubility of light chains are poorly understood, but it can be hypothesized that their amino acid sequence plays an important role. Determining the precise sequences of patient-derived light chains is therefore highly desirable. We establish here a novel de novo sequencing workflow for patient-derived LCs, based on the combination of bottom-up and top-down proteomics without database search. PEAKS is used for the de novo sequencing of peptides that are further assembled into full length LC sequences using ALPS. Top-down proteomics provides the molecular masses of proteoforms and allows the exact determination of the amino acid sequence including all post translational modifications. This pipeline is then used for the complete de novo sequencing of LCs extracted from the urine of 10 patients with multiple myeloma. We show that for the bottom-up part, digestions with trypsin and Nepenthes digestive fluid are sufficient to produce overlapping peptides able to generate the best sequence candidates. Top-down proteomics is absolutely required to achieve 100% final sequence coverage and characterize clinical samples containing several LCs . Our work highlights an unexpected range of modifications.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive Plus

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Immunoglobulin Light Chain Amyloidosis,Multiple Myeloma

SUBMITTER: Martial Rey  

LAB HEAD: Julia Chamot-Rooke

PROVIDER: PXD025884 | Pride | 2021-08-11

REPOSITORIES: Pride