Experiment:  

To prepare protein extracts, cells were re-suspended in an equal volume of lysis buffer (50mM Tris pH 8.0, 50mM NaCl, 1mM EDTA and 1 tablet of Complete Proteinase Inhibitor (Roche)/10ml) 
and incubated on ice for 30 minutes. Cells were then lysed with a dounce homogenizer and the soluble protein extracts obtained after centrifugation. 
For better lysis, 0.05% NP40 was added as a detergent. 

Prior to trypsin digest, detergent was removed using the Orgosol Detergent-Out kit. 

CYS modification: 

YES

Mass spectrometry:

LC-MS/MS on LTQ-Orbitrap

Analysis:

SEQUEST (Bioworks)
Peptide/ProteinProphet v4.0