PXD013314-1

PXD013314 is an original dataset announced via ProteomeXchange.

Title	Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-Labeled Recombinant Protein Fragments Based SRM Assay
Description	Stable isotope-labeled standard (SIS) peptides are used as internal standards in targeted proteomics to provide robust protein quantification, which is required in clinical settings. However, SIS peptides are typically added post trypsin digestion and, as the digestion efficiency can vary significantly between peptides within a protein, the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments called SIS PrESTs. SIS PrESTs are added initially to the sample and SIS peptides are released upon trypsin digestion. The SIS PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. An automated and scalable solid phase extraction workflow for desalting and enrichment of plasma digests was established, enabling simultaneous preparation of up to 96 samples. Robust high-precision quantification of 13 apolipoproteins was achieved using a novel multiplex SIS PrEST-based LC-SRM/MS Tier 2 assay in non-depleted human plasma. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) and was subsequently utilized to investigate the effects of omega-3 carboxylic acids (OM3-CA) andfenofibrate onthese 13 apolipoproteins in human plasma samples from a randomized placebo-controlled trial, EFFECTI (NCT02354976). No significant changes were observed in the OM3-CA arm, while treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS PrESTs can facilitate the generation of robust multiplexed biomarker Tier 2 assays for absolute quantification of proteins in clinical studies.
HostingRepository	PanoramaPublic
AnnounceDate	2019-10-10
AnnouncementXML	Submission_2019-10-10_08:56:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andreas Hober
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	6490 Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-30 23:11:53	ID requested
⏵ 1	2019-10-10 08:56:36	announced

Hober A, Edfors F, Ryaboshapkina M, Malmqvist J, Rosengren L, Percy AJ, Lind L, Forsstr, ö, m B, Uhl, é, n M, Oscarsson J, Miliotis T, Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay. Mol Cell Proteomics, 18(12):2433-2446(2019) [pubmed]

submitter keyword: human, apolipoprotein, omega-3, fenofibrate, hypertriglyceridemia

Fredrik Edfors
contact affiliation	Science for Life Laboratory, KTH - Royal Institute of Technology
contact email	fredrik.edfors@scilifelab.se
lab head
Andreas Hober
contact affiliation	Science for Life Laboratory, KTH - Royal Institute of Technology
contact email	andreas.hober@scilifelab.se
dataset submitter

Panorama Public dataset URI