Influence of variations in sample handling on SELDI-TOF MS serum protein profiles for colorectal cancer

Sample handling can have a profound effect on serum protein profiles, challenging results obtained with archived sera under non-standardized sample collection. Here, we evaluate the influence of variations in sample handling on previous serum protein profiles for colorectal cancer (CRC) (Engwegen et al., World J. Gastroenterol. 2006, 12, 1536-1544). Sera were prospectively obtained from individuals with an indication for colonoscopy (n = 150: 65 controls, 52 adenomatous polyps, 29 CRC, 4 unknown), as well as from normal volunteers (n = 8). Protein profiles were acquired by SELDI-TOF MS on CM10 chips at pH 5. We assessed the influence of Storage temperature, type of collection tube, coagulation temperature and freeze-thaw cycles on the serum protein profile. Several peptides occurred only in samples stored at -20 degrees C, indicating proteolytic degradation during storage. One was a previous CRC biomarker candidate, an N-terminal albumin fragment (m/z 3087), and two others complement C3f and a fragment thereof (m/z 2022 and 1863). Overall differences in protein profiles were also seen for different collection tubes, coagulation temperature and freeze-thaw cycles. However, three of five of our previously defined CRC biomarker candidates are stable to variations in the sample handling protocol, justifying their further validation in prospective studies.