De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma

peer-reviewed · Analytical Chemistry · 2021

peer-reviewed · Analytical Chemistry · 2021. Mathieu Dupré et al. In multiple myeloma diseases, monoclonal immunoglobulin light chains (LCs) are abundantly produced, with, as…

Date	2021-08-03
Type	peer-reviewed
Venue	Analytical Chemistry
Publisher	American Chemical Society (ACS)
Contribution	downstream-application
DOI	10.1021/acs.analchem.1c01955
Citations (OpenAlex)	38
Venue 2-year citedness	7.10

Preprint version: De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma (2021-05-07, ChemRxiv)

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 the kidney, while in other cases remaining soluble up to concentrations of several g·L -1 in plasma. The exact factors crucial for the solubility of LCs are poorly understood, but it can be hypothesized that their amino acid sequence plays an important role. Determining the precise sequences of patient-derived LCs 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 posttranslational 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.

Authors

Methods and tools

Myeloma light chain proteoform sequencing: De novo sequencing of patient-derived monoclonal immunoglobulin light chains in multiple myeloma by combining bottom-up and top-down proteomics without a database.

Data deposited

De novo sequencing of antibody light chain proteoforms from patients with multiple myeloma (as deposited) · PXD025884

Cites (10)

Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme (2021) both
Universal amyloidogenicity of patient-derived immunoglobulin light chains (2021) both
De novo sequencing of proteins by mass spectrometry (2020) both
Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery (2017) both
Complete De Novo Assembly of Monoclonal Antibody Sequences (2016) both
Discrimination of Leucine and Isoleucine in Peptides Sequencing with Orbitrap Fusion Mass Spectrometer (2014) both
De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014) both
Automated de novo protein sequencing of monoclonal antibodies (2008) both
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry (2000) both

Cited by (11)

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