PXD000278-3

PXD000278 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic analysis of breast cancer tissues
Description	We compared label-free and SILAC based quantative methods in combination with shotgun, directed and targeted MS methods in laser capture microdissected breast cancer tissues (biological replicates) as well as whole tissue lysates (technical replicates). We aim to recommend a quantitative method for biomarker discovery and validation in laser capture microdissected tissues. Recorded MS files were analyzed using MaxQuant soft ware (version 1.1.1.36). An initial search was set at a precursor mass window of 7 ppm. The search followed an enzymatic cleavage rule of Trypsin/P and allowed maximal 2 missed cleavage sites. Carbamidomethylati on of cysteines was defined as fixed modification, while protein N;terminal acetylation and methionine oxidation were defined as variable modifications for database searching. To construct the MS/MS peak list file, up to top 8 peaks per 100 Da window were extracted and submitted to search against a concatenated forward and reverse version of the UniProtKB/Swiss;Prot human database (generated from version 2011_03). The cutoff of global false discovery rate (FDR) for peptide and protein identification was set to 0.01, and only peptides with greater than or equal to 7 amino acid residues were allowed for identification. Minimally one unique peptide was required for protein identification
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:17:33.831.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ning Qing Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-06-10 02:43:42	ID requested
1	2013-08-23 02:16:18	announced
1	2014-07-25 01:14:35	announced
2	2013-08-23 02:19:38	announced	Add reference
⏵ 3	2024-10-22 04:17:34	announced	2024-10-22: Updated project metadata.

Liu NQ, Dekker LJ, Stingl C, G, ü, zel C, De Marchi T, Martens JW, Foekens JA, Luider TM, Umar A, Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches. J Proteome Res, 12(10):4627-41(2013) [pubmed]

10.1021/pr4005794;

submitter keyword: human breast cancer, nanoLC-Orbitrap-MS, laser capture microdissection,quantitative proteomics

Ning Qing Liu
contact affiliation	Radboud Institute of Molecular Life Sciences
contact email	n.liu@ncmls.ru.nl
lab head
Ning Qing Liu
contact affiliation	Radboud Institute of Molecular Life Sciences
contact email	n.liu@ncmls.ru.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000278
     1. Label: PRIDE project
     2. Name: Quantitative proteomic analysis of breast cancer tissues