Project PXD000246



Human breast cancer cell line LC-MS/MS


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.

Sample Processing Protocol

See details in reference(s) : 24317253

Data Processing Protocol

See details in reference(s) : 24317253


Jacob Kennedy, Fred Hutchinson Cancer Research Center

Submission Date


Publication Date



Not available


LTQ Orbitrap Velos


Not available


Not available

Experiment Type

Bottom-up proteomics


    Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods. 2014 Feb;11(2):149-55 PubMed: 24317253