SELDI-TOF MS has been demonstrated as a powerful tool for biomarker discovery. However, a major disadvantage of SELDI-TOF MS is the lack of direct identification of the discriminatory peaks discovered. We describe a novel experimental identification strategy where peptides/proteins captured to a weak cation exchange ProteinArray surface (CM10) are eluted, and thereafter identified by utilizing a sensitive LC–MS/MS (i.e. LTQ Orbitrap). A mixture of four known proteins was used to test the novel experimental approach described, and all four proteins were successfully identified. Additionally, a biomarker candidate previously discovered in plasma of Atlantic cod (Gadus morhua) by SELDI-TOF MS was identified. Thus, this study indicated that a combination of on-chip elution and a highly sensitive LC–MS/MS system can be an alternative approach to identify biomarker candidates discovered by use of SELDI-TOF MS. ► Proteins were eluted off a ProteinChip and subsequently identified using LC–MS/MS. ► A biomarker candidate from a SELDI-TOF MS study was identified using this approach. ► A potential alternative approach to identify protein forms detected by SELDI-TOF MS.