Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS).
BACKGROUND
Issues have been raised concerning the robustness and validity of alleged serum markers discovered by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS). Pre-analytical variables have been shown to exert a profound effect on protein profiles, irrespective of true biological variation. However, little is known about the possible effects of sample storage duration on protein profiles. We, therefore, aimed to investigate the effects of extended storage duration on the serum protein profile.


METHODS
Archival sera from 140 breast cancer patients, stored at -30 degrees C for 1-11 years, were profiled by SELDI-TOF MS using immobilised metal affinity capture (IMAC) arrays, a condition applied in the majority of breast cancer biomarker discovery studies.


RESULTS
Fourteen peak clusters, structurally identified as C3a des-arginine anaphylatoxin and multiple fragments of albumin and fibrinogen, were found to be significantly associated with sample storage duration by five distinct patterns. These proteins have been described previously as potential cancer markers, rendering them specific to both disease and sample handling issues.


CONCLUSIONS
To prevent experimental variation being interpreted erroneously as disease associated variation, assessment of potential confounding pre-analytical parameters is a pre-requisite in biomarker discovery and validation studies. In addition, with respect to the different (non-)linear patterns observed in the current study, simply performing linear corrections to account for sample storage duration will not necessarily suffice.
Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute/Slotervaart Hospital, Amsterdam, The Netherlands. Marie-Christine.Gast@slz.nl
Marie-Christine W
MC
Gast
Carla H
CH
van Gils
Lodewijk F A
LF
Wessels
Nathan
N
Harris
Johannes M G
JM
Bonfrer
Emiel J Th
EJ
Rutgers
Jan H M
JH
Schellens
Jos H
JH
Beijnen
D000368:Aged; D000595:Amino Acid Sequence; D014408:Biomarkers, Tumor / Q000097:blood*; D001798:Blood Proteins / Q000032:analysis*; D001943:Breast Neoplasms / Q000175:diagnosis; D005260:Female; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D055550:Protein Stability; D040901:Proteomics / Q000379:methods* / Q000592:standards; D013048:Specimen Handling / Q000379:methods* / Q000592:standards; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013997:Time Factors
D014408:Biomarkers, Tumor; D001798:Blood Proteins