PXD046072 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| 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 | 2024-08-09 |
| AnnouncementXML | Submission_2024-08-09_03:42:46.429.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 |
Dataset History
| 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. |
Publication List
| 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; |
Keyword List
| submitter keyword: peptide fractionation,Antibody, mass spectrometry, immune repertoire, multi-dimensional chromatography, ion-mobility, bottom-up proteomics, de novo sequencing, plasma proteomics |
Contact List
| 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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD046072
- Label: PRIDE project
- Name: Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques.
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