title: Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines.
abstract: As a direct consequence of the high diversity of the aggressive blood cancer acute myeloid leukemia (AML), proteomic samples from patients are strongly heterogeneous, rendering their accurate relative quantification challenging. In the present study, we investigated the benefits of using a super-SILAC mix of AML derived cell lines as internal standard (IS) for quantitative shotgun studies. The Molm-13, NB4, MV4-11, THP-1, and OCI-AML3 cell lines were selected for their complementarity with regard to clinical, cytogenetic, and molecular risk factors used for prognostication of AML patients. The resulting IS presents a high coverage of the AML proteome compared to single cell lines allied with high technical reproducibility, thus enabling its use for AML patient comparison. This was confirmed by comparing the protein regulation between the five cell lines and by applying the IS to patient material; hence, we were able to reproduce specific functional regulations known to be related to disease progression and molecular genetic abnormalities. The MS proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD000441.
authors.affiliation: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
authors.forename: Elise
authors.initials: E
authors.lastname: Aasebø
authors.forename: Marc
authors.initials: M
authors.lastname: Vaudel
authors.forename: Olav
authors.initials: O
authors.lastname: Mjaavatten
authors.forename: Gro
authors.initials: G
authors.lastname: Gausdal
authors.forename: Arthur
authors.initials: A
authors.lastname: Van der Burgh
authors.forename: Bjørn Tore
authors.initials: BT
authors.lastname: Gjertsen
authors.forename: Stein Ove
authors.initials: SO
authors.lastname: Døskeland
authors.forename: Oystein
authors.initials: O
authors.lastname: Bruserud
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: Frode
authors.initials: F
authors.lastname: Selheim
mesh_terms: D014408:Biomarkers, Tumor; D045744:Cell Line, Tumor; D006801:Humans; D007553:Isotope Labeling; D015470:Leukemia, Myeloid, Acute / Q000378:metabolism*; D013058:Mass Spectrometry / Q000379:methods*; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome
keywords: Acute myeloid leukemia; Biomedicine; Cell lines; Super-SILAC