PXD055846

PXD055846 is an original dataset announced via ProteomeXchange.

Title	Benchmarking of mass spectrometry-based antibody repertoire profiling reveals extensive systematic biases
Description	The serum antibody repertoire is crucial for long-term immune protection, holding significant immunological and biotechnological value. Bottom-up proteomics is the most widely used mass spectrometry (MS) technique for profiling the sequence diversity of serum antibodies. However, serum antibody bottom-up proteomics (Ab-seq) has not been thoroughly benchmarked. In this study, we quantified the replicability and robustness of Ab-seq using six monoclonal antibodies with known protein sequences in 70 concentration and polyclonality combinations with and without polyclonal blood IgG background. Each combination underwent four protease treatments and was analyzed across four experimental and three technical replicates (3,360 LC-MS/MS runs). We quantified the dependence of MS-based antibody sequence identification on antibody sequence as well as concentration, protease, background signal diversity, and bioinformatics setup. Integrating experimental replicates, multiple proteases, and bioinformatics tools enhanced antibody identification. De novo peptide sequencing further improved sequence identification, complementing database-dependent methods. Our work provides a foundational resource for the field of MS-based serum antibody profiling.
HostingRepository	PRIDE
AnnounceDate	2025-12-04
AnnouncementXML	Submission_2025-12-04_07:42:03.997.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ingrid Maria Erika Ekman Stensland
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-13 05:16:41	ID requested
⏵ 1	2025-12-04 07:42:04	announced

10.1016/J.CELS.2025.101449;

submitter keyword: serum antibody bottom-up proteomics (Ab-seq), MS, antibody sequencing, serum antibody repertoire

Tuula Anneli Nyman
contact affiliation	Head of the Proteomics Core Facility, NAPI project manager, Institute of Immunology Rikshospitalet, Oslo, Norway
contact email	tuula.nyman@medisin.uio.no
lab head
Ingrid Maria Erika Ekman Stensland
contact affiliation	Oslo University hospital
contact email	maria.stensland@medisin.uio.no
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/2025/12/PXD055846

PRIDE project URI

• PRIDE
  1. PXD055846
     1. Label: PRIDE project
     2. Name: Benchmarking of mass spectrometry-based antibody repertoire profiling reveals extensive systematic biases