Dataset Information

Human breast cancer cell line LC-MS/MS

ABSTRACT: Human breast cancer cell lines were pooled according to ER/Her2 status. The whole cell lysate samples were reduced and treated with iodoacetamide and then digested with trypsin. The samples were separated into 6 fractions by online high pH reverse-phase fractionation and then analyzed by reverse-phase chromatography coupled to a Thermo LTQ-Orbitrap Velos mass spectrometer. MS/MS files were searched against version 3.69 of the Human International Protein Index (IPI) sequence database with decoy sequences by the X!Tandem database search engine with k-score plugin with the following parameters: tryptic enzyme constraint allowing for up to two missed cleavages. Peptide MH+ mass tolerances set at 2.0 Da with post search filtering of precursor mass to 50 ppm. Oxidized methionine as a variable modification and carbamidomethylated cysteine as a static modification. FDR < 0.005 based on decoy search.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jacob Kennedy

PROVIDER: PXD000246 | Pride | 2013-10-18

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Site1_Cell_line_ERneg_HER2neg_Pool1_1D_Rep1.raw	Raw
	Site1_Cell_line_ERneg_HER2neg_Pool1_1D_Rep2.raw	Raw
	Site1_Cell_line_ERneg_HER2neg_Pool1_1D_Rep3.raw	Raw
	Site1_Cell_line_ERneg_HER2neg_Pool1_1D_Rep4.raw	Raw
	Site1_Cell_line_ERneg_HER2neg_Pool1_1D_Rep5.raw	Raw

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Publications

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.

Kennedy Jacob J JJ Abbatiello Susan E SE Kim Kyunggon K Yan Ping P Whiteaker Jeffrey R JR Lin Chenwei C Kim Jun Seok JS Zhang Yuzheng Y Wang Xianlong X Ivey Richard G RG Zhao Lei L Min Hophil H Lee Youngju Y Yu Myeong-Hee MH Yang Eun Gyeong EG Lee Cheolju C Wang Pei P Rodriguez Henry H Kim Youngsoo Y Carr Steven A SA Paulovich Amanda G AG

Nature methods 20131208 2

Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays rep ...[more]

PMID: 24317253

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