PXD046072

PXD046072 is an original dataset announced via ProteomeXchange.

Title	Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.
Description	Circulating antibodies provide valuable information about an individual’s immune status and constitute a significant portion of the human plasma proteome. Proteomic analysis of plasma is challenged by the large dynamic concentration range of plasma proteins, including antibodies. Peptide fractionation prior to data-independent (shotgun) proteomics has the potential to overcome this obstacle and enable increased coverage of plasma proteins. In this work, we evaluated the detection of tryptic immunoglobulin variable region peptides using multidimensional chromatography (high-pH preparative LC) or gas-phase ion mobility spectrometry (FAIMS). Typical digests of eight serum samples were obtained by (a) direct LC-MS (without prior fractionation, 1D), (b) LC-FAIMS-MS, and (c) high-pH reversed-phase fractionation into 24 fractions and subsequent measurement of each fraction. As de novo search is an essential step in antibody variable region peptide identification, all MS/MS spectra were acquired in high resolution Orbitrap mode.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:53:44.141.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046072
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christoph Stingl
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-11 14:36:09	ID requested
1	2024-08-09 03:42:47	announced
⏵ 2	2024-10-22 06:53:45	announced	2024-10-22: Updated project metadata.

Stingl C, VanDuijn MM, Dejoie T, Sillevis Smitt PAE, Luider TM, Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques. Cell Rep Methods, 4(6):100795(2024) [pubmed]

10.1016/j.crmeth.2024.100795;

10.6019/PXD046072;

submitter keyword: peptide fractionation,Antibody, mass spectrometry, immune repertoire, multi-dimensional chromatography, ion-mobility, bottom-up proteomics, de novo sequencing, plasma proteomics

Theo M. Luider
contact affiliation	Head of Laboratory of Neuro-Oncology, Neurology, Clinical & Cancer Proteomics
contact email	t.luider@erasmusmc.nl
lab head
Christoph Stingl
contact affiliation	Erasmus MC Rotterdam Department of Neurology
contact email	c.stingl@erasmusmc.nl
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/2024/08/PXD046072

PRIDE project URI

• PRIDE
  1. PXD046072
     1. Label: PRIDE project
     2. Name: Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.