PXD000578-3

PXD000578 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometry-based quantitative proteomics of whole cell lysate from breast cancer cell line MCF7 spiked with 57 protein standards
Description	Here we present quantitative proteomics data used in the evaluation of quantitative accuracy. A human cell line, MCF7 was split into 9 aliquotes that were spiked with a dilution series of 57 protein standards of known amounts spanning 5 orders of magnitude. The protein extracts were trypsinized, and the peptides were analysed by LC-MS using either a label-free or a label-based (TMT 6-plex and iTRAQ 8-plex) quantification approach. The iTRAQ- and TMT-labelled samples were co-analysed and separated by HiRIEF (high resolution isoelectric focusing) prior LC-MS. Raw MS data was identified and quantified under the software platform Proteome Discoverer 1.3.0.339 (Thermo Fisher Scientific Inc.) or MaxQuant software (version 1.2.0.18) (label-free data). For both protein identification and quantification at least 1 unique (i.e. a peptide that occurs in not more than one database entry) peptide was required. The false discovery rate (FDR) for peptide identification was set to 5% in all analyses. For the iTRAQ and TMT labeled samples, all MS/MS spectra were searched by SEQUEST combined with the Percolator algorithm (version 2.0) for PSM search optimization. Searches were performed against a custom made database consisting of SwissProt human sequences(uniprot.org 2012-01-17, 20242 entries), and the spiked in protein standards (57 protein sequences). Peptide FDR was calculated by a target – decoy approach.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:17:39.187.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	AnnSofi Sandberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iTRAQ8plex:13C(6)15N(2); TMT6plex; iTRAQ8plex; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-11-13 01:22:24	ID requested
1	2013-12-03 07:20:18	announced
1	2013-12-03 07:21:14	announced
2	2014-07-25 01:46:57	announced	Updated project metadata.
⏵ 3	2024-10-22 04:17:39	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2013.10.035;

Sandberg A, Branca RM, Lehti, ö J, Forshed J, Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference. J Proteomics, 96():133-44(2014) [pubmed]

submitter keyword: LC-MS,quantification,MCF7,isoelectric focusing,iTRAQ,TMT,precursor mixing

AnnSofi Sandberg
contact affiliation	Clinical Proteomics Unit, Dep. of Oncology-Pathology
contact email	annsofi.sandberg@ki.se
lab head
AnnSofi Sandberg
contact affiliation	Clinical Proteomics Unit, Dep. of Oncology-Pathology
contact email	annsofi.sandberg@ki.se
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/2013/12/PXD000578

PRIDE project URI

• PRIDE
  1. PXD000578
     1. Label: PRIDE project
     2. Name: Mass spectrometry-based quantitative proteomics of whole cell lysate from breast cancer cell line MCF7 spiked with 57 protein standards