PXD046550

PXD046550 is an original dataset announced via ProteomeXchange.

Title	Longitudinal fluctuations in protein concentrations and higher-order structures in the plasma proteome of patients enduring a kidney transplant: two in-depth case studies
Description	Using proteomics and complexome profiling we studied longitudinal variations in the plasma proteome of two kidney transplant recipients, prior to and after their transplantation, in comparison to two healthy controls. Their post-transplant course was complicated with several bacterial infections, resulting in dramatic changes in the plasma proteome, especially in acute phase protein concentrations. As positive acute phase proteins, being elevated upon inflammation, we observed the well-known C-reactive protein (CRP) and Serum Amyloid A (SAA1 and SAA2), but also Fibrinogen (FGA, FGB and FGG), Haptoglobin (HP), Leucine-rich alpha-2-glycoprotein (LRG1), Lipopolysaccharide-binding protein (LBP), Alpha-1-antitrypsin (SERPINA1), Alpha-1-antichymotrypsin (SERPINA3), Protein S100 (S100A8, S100A9), Complement protein C4, C4b-binding protein alpha chain (C4BPA), Complement factor B (CFB) and Monocyte differentiation antigen CD14. As negative acute phase proteins, being downregulated upon inflammation, we identified the well-documented Serotransferrin (TF) and Transthyretin (TTR), but also Kallistatin (SERPINA4), Heparin cofactor 2 (SERPIND1), Inter-alpha-trypsin inhibitor heavy chain H1 and H2 (ITIH1, ITIH2). For patient P2, who showed the most severe acute phase response, we additionally performed plasma complexome profiling by SEC-LC-MS on all longitudinal samples. We observe that several plasma proteins displaying alike concentration patterns, co-elute and possibly form macromolecular complexes. These include a) FGA, FGB and FGG (naturally, b) ITIH1 and ITIH2, c) HP and Hemoglobin (HB), d) the small acute phase biomarker proteins SAA1 and SAA2 with the Apolipoproteins A-I, A-II, A-IV (APOA1, APOA2, APOA4). By complexome profiling we expose how SAA1 and SAA2 likely become incorporated into high-density lipid particles, thereby replacing partly APOA1 and APOA4. Overall, our data highlight that the combination of in-depth longitudinal plasma proteome and complexome profiling can shed further light on the correlated variations in the abundance of several plasma proteins upon inflammatory events.
HostingRepository	PRIDE
AnnounceDate	2024-05-07
AnnouncementXML	Submission_2024-05-06_19:38:11.664.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sofia Kalaidopoulou Nteak
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-31 17:45:52	ID requested
⏵ 1	2024-05-06 19:38:12	announced

Kalaidopoulou Nteak S, V, ö, llmy F, Lukassen MV, van den Toorn H, den Boer MA, Bondt A, van der Lans SPA, Haas PJ, van Zuilen AD, Rooijakkers SHM, Heck AJR, Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant. J Proteome Res, 23(6):2124-2136(2024) [pubmed]

10.1021/acs.jproteome.4c00064;

submitter keyword: acute phase, bottom-up MS,plasma, medical proteomics, complexome profiling

Albert J.R.
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands and Netherlands Proteomics Center, Utrecht, The Netherlands
contact email	A.J.R.Heck@uu.nl
lab head
Sofia Kalaidopoulou Nteak
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Utrecht University
contact email	s.kalaidopoulounteak@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD046550
     1. Label: PRIDE project
     2. Name: Longitudinal fluctuations in protein concentrations and higher-order structures in the plasma proteome of patients enduring a kidney transplant: two in-depth case studies