PXD013415

PXD013415 is an original dataset announced via ProteomeXchange.

Title	Quantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS)
Description	Quantification 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.
HostingRepository	PRIDE
AnnounceDate	2021-04-12
AnnouncementXML	Submission_2021-04-12_15:38:57.312.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD013415
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Horvatovich Péter
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-04-09 03:13:03	ID requested
⏵ 1	2021-04-12 15:38:59	announced

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]

submitter keyword: Biomarker, COPD, Immunoprecipitation, LC-MS, Methionine oxidation, Quantification

Peter Horvatovich
contact affiliation	Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
contact email	p.l.horvatovich@rug.nl
lab head
Horvatovich Péter
contact affiliation	Faculty of Mathematics and Natural Sciences, Department of Pharmacy, Analytical Biochemistry, University of Groningen, 9713 AV Groningen, The Netherlands
contact email	p.l.horvatovich@rug.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD013415
     1. Label: PRIDE project
     2. Name: Quantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS)