PXD025884

PXD025884 is an original dataset announced via ProteomeXchange.

Title	De novo sequencing of antibody light chain proteoforms from patients with multiple myeloma
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-02-14
AnnouncementXML	Submission_2022-02-13_16:23:43.927.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martial Rey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-07 09:46:20	ID requested
1	2021-08-11 00:45:35	announced
⏵ 2	2022-02-13 16:23:44	announced	2022-02-14: Updated project metadata.

Dupr, é M, Duchateau M, Sternke-Hoffmann R, Boquoi A, Malosse C, Fenk R, Haas R, Buell AK, Rey M, Chamot-Rooke J, Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma. Anal Chem, 93(30):10627-10634(2021) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: proteoforms, top-down proteomics,antibody, bottom-up proteomics, de novo sequencing, light chain disease

Julia Chamot-Rooke
contact affiliation	Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, 75015 Paris, France
contact email	julia.chamot-rooke@pasteur.fr
lab head
Martial Rey
contact affiliation	CNRS, Pasteur
contact email	martial.rey@pasteur.fr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/08/PXD025884

PRIDE project URI

• PRIDE
  1. PXD025884
     1. Label: PRIDE project
     2. Name: De novo sequencing of antibody light chain proteoforms from patients with multiple myeloma