PXD007191

PXD007191 is an original dataset announced via ProteomeXchange.

Title	Optimising sample preparation of the plasma peptidome
Description	We further expanded on previous optimizations to isolate the plasma peptidome and compared various methods to maximize identifications with speed and ease. Previous studies have reported loss of polypeptides binding to high abundant proteins during depletion strategies. We hypothesized that rapid chaotropic denaturation of plasma with urea under reducing conditions would liberate non-covalently bound peptides to improve recovery during protein depletion. We also compared depletion strategies to isolate the peptidome including protein precipitation and removal with either TCA, acetone or acetonitrile (AcN). Following centrifugation of precipitated proteins, the supernatant containing peptides was collected. For acetone and AcN precipitations, an additional vacuum centrifugation step was required followed by resuspension of peptides in aqueous buffer. Our comparison of peptidome isolation also included removal of proteins with size-exclusion 10 kDa MWCO filters. All peptide isolations were acidified to 0.1% TFA, adjusted to 5% acetonitrile and desalted with HLB-SPE. Peptides were analysed by single-shot nanoUHPLC-MS/MS employing both HCD and EThcD and quantified by LFQ
HostingRepository	PRIDE
AnnounceDate	2017-10-09
AnnouncementXML	Submission_2017-10-09_02:32:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Benjamin Parker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	amidated residue; monohydroxylated residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-04 04:29:18	ID requested
⏵ 1	2017-10-09 02:32:15	announced

Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski JFP, Richter EA, James DE, Multiplexed Temporal Quantification of the Exercise-regulated Plasma Peptidome. Mol Cell Proteomics, 16(12):2055-2068(2017) [pubmed]

curator keyword: Technical

submitter keyword: peptidomics, plasma, sample preparation

Benjamin Parker
contact affiliation	The University of Sydney
contact email	benjamin.parker@sydney.edu.au
lab head
Benjamin Parker
contact affiliation	The University of Sydney
contact email	benjamin.parker@sydney.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007191
     1. Label: PRIDE project
     2. Name: Optimising sample preparation of the plasma peptidome