PXD000661

PXD000661 is an original dataset announced via ProteomeXchange.

Title	A ‘proteomic ruler’ for protein copy number and concentration estimation without spike-in standards
Description	Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting and protein concentration measurements. Here we present a novel concept that delivers similar quantitative results directly from deep eukaryotic proteome datasets without any additional experimental steps. We show that the MS-signal of histones can be used as a ‘proteomic ruler’ because is proportional to the amount of DNA in the sample, which in turn depends of the number of cells. As a result, our proteomic ruler approach adds an absolute scale to the MS readout and allows the estimation of the copy numbers of individual proteins per cell. We compare our protein quantifications with values derived from the SILAC-PrEST method, which combines spike-in protein fragment standards with precise isotope label quantification. The proteomic ruler approach yields quantitative readouts that are in remarkably good agreement with the precision method. We attribute this surprising result to the fact that the proteomic ruler approach omits error-prone steps such as cell counting or protein concentration measurements. The proteomic ruler approach is readily applicable to any deep eukaryotic proteome dataset – even in retrospect analysis – and we demonstrate its usefulness on a series of mouse organ proteomes.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_02:52:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap; LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2013-12-19 02:49:48	ID requested
1	2014-09-16 19:26:30	announced
2	2014-09-17 02:12:48	announced	Updated publication reference for PubMed record(s): 25225357.
⏵ 3	2014-10-23 02:52:35	announced	Updated project metadata.

Wi, ś, niewski JR, Hein MY, Cox J, Mann M, A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards. Mol Cell Proteomics, 13(12):3497-506(2014) [pubmed]

curator keyword: Technical, Highlighted

submitter keyword: absolute quantification, copy numbers

Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2014/09/PXD000661

PRIDE project URI

• PRIDE
  1. PXD000661
     1. Label: PRIDE project
     2. Name: A ‘proteomic ruler’ for protein copy number and concentration estimation without spike-in standards