At present, multiple myeloma (MM) remains an incurable disease and cologenic cells may be responsible fordisease relapse. It has been proposed that CD20+/CD138- NCI-H929 cells could be hallmarks of MM clonogeniccells. Here, the immunology phenotype of NCI-H929 cells is described. Only a small population of CD20+/CD138- cells (<1%) was found in the NCI-H929 cell line, but CD20+/CD138- cells were not detected. We foundthat CD20+/CD138+ cells were able to exhibit cologenic capacity by colony formation assay and continuouspassage culture. Proteins were analyzed by 1D-SDS-PAGE and TMT based quantitative differential liquidchromatography tandem mass spectrometry (LC-MS/MS). 1,082 non-redundant proteins were identified, 658 ofwhich were differentially expressed with at least a 1.5-fold difference. 205 proteins in CD20+ cells were expressedat higher levels and 453 proteins were at lower levels compared with CD20- cells. Most proteins had catalytic andbinding activity and mainly participated in metabolic processes, cell communication and molecular transport.These results proved that there are different biological features and protein expression profile between CD20+and CD20- cells in the NCI-H929 cell line.