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

Not available

Data Processing Protocol

Not available


Jacob Kennedy, Clinical Research Division

Submission Date



Not available


LTQ Orbitrap Velos


Not available


Not available

Experiment Type

Bottom-up proteomics


Publication pending

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