Chronic myeloid leukaemia (CML) is characterised by a reciprocal translocation t(9;22)(q34;q11) which leads to the production of the BCR-ABL1 protein tyrosine kinase (De Keersmaecker & Cools, 2006). In the chronic phase, the disease is maintained by BCR-ABL1 activity and responds well to treatment with tyrosine kinase inhibitor therapy (Giles et al, 2005). To improve the understanding of the biology of CML, we used surface enhanced laser desorption/ionization time of flight (SELDI-TOF) mass spectrometry to identify diseasespecific serum proteins.Serum samples were collected from 23 CML patients at presentation (CML-P), median age 46 years (range 21-85), male:female 1AE3:1, median spleen size 7 cm (range 5-23), mean white cell count 135 · 10 9 /l (range 35-665) and mean absolute neutrophil count 102 · 10 9 /l (range 25-235). Median duration of Gleevec therapy (n = 27) until haematological remission (World Health Organization criteria) was achieved was 20 months (range 6-51). Seven additional paired samples were available from patients at diagnosis and following the induction of HR. Subjects with neutrophilia due to nonmalignant causes (n = 24) (absolute neutrophil count >15 · 10 9 /l) were analysed as a control group and compared the results to age and sex matched normal donors (n = 34). Serum was stored in multiple aliquots at )80°C for single use. A Biomek 2000 liquid handling station was used to prepare arrays and bind samples in duplicate. Immobilised metal affinity chromatography arrays (Ciphergen, Guildford, UK) were used and scanned on a PCS 4000 (Ciphergen) time of flight mass spectrometer using 9000 and 20 000 Da focus masses (deflector: 1500 Da). Peaks were automatically detected using Ciphergen Express 3.0 (CE 3) software following manufacturer's instructions. Useful peaks for cluster analysis were selected with a signal:noise of ‡3, resolution between 300 and 400 and confirmed visually.Informative m/z peaks were enriched by pH fractionation of pooled sera (n = 8) using anion exchange chromatography (Q HyperD F, Ciphergen) or reverse phase chromatography and concentrated using either YM-30 or YM-50 filters (Millipore, Livingstone, UK) followed by one dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Coomasie-stained bands were excised and either passively eluted to confirm the correct m/z peak or subjected to in-gel trypsinization (Roche, UK) on NP-20 arrays (Delbosc et al, 2008). Peptides which could not be enriched for peptide mass fingerprinting were directly identified by fragmentation on the Micromass Q-TOF2 instrument. Unique peptide mass fingerprints were matched to in silico trypsin digested protein signatures using MASCOT (http://www.matrixscience.com). The most abundant peptide was fragmented to confirm protein identity (PCI 1000 tandem MS interface with a Q-TOF2; Micromass, Manchester, UK).Thirty-eight clusters of serum protein peaks from 2AE5 to 50 kDa were annotated in CML-P, normal and neutrophilia patients, CE 3.0 was used to perform univariate data analysis. Receive...