⮝ Full datasets listing

PXD013415

PXD013415 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleQuantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS)
DescriptionQuantification of intact proteins in complex biological matrices by liquid chromatography-mass spectrometry (LC-MS) is a promising analytical strategy but is technically challenging, notably for concentrations at or below the ng/mL level. Therefore, MS-based protein quantification is mostly based on measuring protein-specific peptides, so-called ‘surrogate peptides’, that are released through proteolysis. While quantitative protein bioanalysis based on peptide LC-MS is much more sensitive, not every peptide is suitable in this respect. For example, some peptides are too small to be unique for a protein while others are too large to be measured with sufficient sensitivity, so careful selection of appropriate peptides is essential. Here we present a validated LC-MS method for quantification of surfactant protein D (SPD) at clinically relevant levels between 5 and 500 ng/mL using 50 microliters of serum. This method targets two SPD-specific peptides in the C-type lectin, ligand binding domain of the SPD protein. One of these peptides contains a methionine residue which would typically be avoided because of its unstable nature. Some quantitative methods do target methionine-containing peptides, and corresponding workflows feature an oxidation step at the peptide level using hydrogen peroxide (H2O2) to convert all methionine residues to more stable methionine sulfoxides. For our method, such a procedure was associated with peptide loss, hence we developed an oxidation procedure at the protein level using H2O2 to oxidize methionine residues and the enzyme catalase to quench excess H2O2. This procedure may be applicable to other quantitative methods based on a surrogate peptide-based approach and may potentially also be useful for MS-based workflows targeting intact proteins.
HostingRepositoryPRIDE
AnnounceDate2021-04-12
AnnouncementXMLSubmission_2021-04-12_15:38:57.312.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD013415
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterHorvatovich Péter
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListOxidation; Carbamidomethyl
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-04-09 03:13:03ID requested
12021-04-12 15:38:59announced
Publication List
Klont F, Pouwels SD, Bults P, van de Merbel NC, Ten Hacken NHT, Horvatovich P, Bischoff R, Quantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS). Talanta, 202():507-513(2019) [pubmed]
Keyword List
submitter keyword: Biomarker, COPD, Immunoprecipitation, LC-MS, Methionine oxidation, Quantification
Contact List
Peter Horvatovich
contact affiliationDepartment of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
contact emailp.l.horvatovich@rug.nl
lab head
Horvatovich Péter
contact affiliationFaculty of Mathematics and Natural Sciences, Department of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
contact emailp.l.horvatovich@rug.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/2021/04/PXD013415
PRIDE project URI
Repository Record List
[ + ]