PXD008969

PXD008969 is an original dataset announced via ProteomeXchange.

Title	AS precipitation and protein A affinity chromatography for abundant plasma protein depletion
Description	Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protein concentrations, a tandem depletion technique consisting of ammonium sulfate precipitation and Protein A affinity chromatography was developed. Using this method, 50 % of albumin, together with other high abundant proteins such as alpha-1-antitrypin, was depleted from the plasma sample at 20 % to 40 % ammonium sulfate saturation levels. In combination with immunoglobulin removal using a Protein A column, this technique delivered up to 40 new low- to medium abundance protein identifications when performing a shotgun mass spectrometry analysis. Compared to non-depleted plasma, 270 additional protein spots were observed during 2D-PAGE analysis. These results illustrate that this tandem depletion method is equivalent to commercial kits which are based on immune-affinity chromatography. Moreover, this method using protein A immunoglobulin depletion was shown to be highly reproducible and a minimal amount of non-target proteins was depleted. The combination of ammonium sulfate precipitation and Protein A affinity chromatography offers a low cost, efficient, straightforward and reproducible alternative to commercial kits, with proteins remaining in native conformation, allowing protein activity and protein interaction studies.
HostingRepository	PRIDE
AnnounceDate	2018-05-08
AnnouncementXML	Submission_2018-05-08_00:42:24.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008969
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Lentel Pringels
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	HNE; Hex(1)HexNAc(1)dHex(1); Bacillosamine; Crotonyl; Hex; SPITC; Hex(1)HexNAc(2)Pent(1); Methylphosphonate; Delta:H(4)C(2)O(-1)S(1); CAMthiopropanoyl; DFDNB; Propionamide; LeuArgGlyGly; Deamidated; Methylpyrroline; Methylamine; DTT_ST; CHDH; Myristoyl; Cation:K; Delta:H(2)C(5); dHex(1)Hex(3)HexNAc(4); Octanoyl; Gln->pyro-Glu; Met->Hsl; Diethylphosphate; Guanidinyl; Menadione-HQ; BHTOH; Fluoro; Ammonia-loss; Ethylphosphate; ISD_z+2_ion; Oxidation; Piperidine; AEC-MAEC; Ethanedithiol; Carboxy; Met->Hpg; O-pinacolylmethylphosphonate; BITC; 4-ONE; PET; Ethanolamine; Cation:Na; Hex(1)HexNAc(2)dHex(1)Pent(1); maleimide3; Hydroxytrimethyl; PyMIC; Trp->Hydroxykynurenin; Sulfo; MG-H1; GlyGly; Deoxy; 3-phosphoglyceryl; Malonyl; Formyl; Carbamyl; LG-anhydrolactam; Delta:H(2)C(3)O(1); Cation:Mg[II]; Thiophospho; PhosphoHexNAc; Tyr->Dha; NDA; Ammonium; Dimethyl; Lipoyl; Cation:Cu[I]; Hypusine; Pro->Pyrrolidone; Crotonaldehyde; NeuAc; Dethiomethyl; Cytopiloyne; Amidated; Thioacyl; Diethyl; Hex(3)HexNAc(2); Lys->AminoadipicAcid; Pro->pyro-Glu; Ethanolyl; Phospho; Cation:Zn[II]; PEITC; Propargylamine; Acetyl; cGMP; Cation:Ni[II]; Nitro; ADP-Ribosyl; 2HPG; Methylthio; dichlorination; Carboxymethyl; 4-ONE+Delta:H(-2)O(-1); Cation:Ag; Hex1HexNAc1; HexNAc; Carbamidomethyl; Cation:Ca[II]; 3sulfo; Biotin-PEO-Amine; HNE+Delta:H(2); cGMP+RMP-loss; Glu->pyro-Glu; Arg->Npo; Carboxyethyl; MercaptoEthanol; Hydroxymethyl; EDT-maleimide-PEO-biotin; Delta:H(2)C(2); Ethyl; Cation:Li; O-Isopropylmethylphosphonate; Cation:Fe[II]; phosphoRibosyl; Isopropylphospho; Methyl; AEBS; Pyridylacetyl; Methylmalonylation; Glucosylgalactosyl; Pyridylethyl; Ethoxyformyl; TNBS; Didehydro; Cytopiloyne+water; Pro->Pyrrolidinone; Dansyl; Iminobiotin; SMA; HexN; Diisopropylphosphate; Hex(2)HexNAc(2)Pent(1); DimethylpyrroleAdduct; Lys->Allysine; LG-anhyropyrrole; Amidine; ethylamino; maleimide; Dehydrated; Biotin; Dioxidation; Ethyl+Deamidated; Benzoyl; Carbofuran; glycidamide
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-16 03:20:12	ID requested
⏵ 1	2018-05-08 00:42:25	announced

Mahn A, Ismail M, Depletion of highly abundant proteins in blood plasma by ammonium sulfate precipitation for 2D-PAGE analysis. J Chromatogr B Analyt Technol Biomed Life Sci, 879(30):3645-8(2011) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Plasma, mouse, abundant protein depletion

Liliane Schoofs
contact affiliation	KULeuven, Leuven, Belgium
contact email	liliane.schoofs@kuleuven.be
lab head
Lentel Pringels
contact affiliation	KULeuven
contact email	lentel.pringels@kuleuven.be
dataset submitter

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/2018/05/PXD008969

PRIDE project URI

• PRIDE
  1. PXD008969
     1. Label: PRIDE project
     2. Name: AS precipitation and protein A affinity chromatography for abundant plasma protein depletion