Received on November 8, 2006
Accepted on March 1, 2007

Proteomics and Protein Markers

Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry

¹ Glostrup Research Institute, Glostrup Hospital, Glostrup, Denmark

^* To whom correspondence should be addressed. E-mail: jakalb01{at}glostruphosp.kbhamt.dk.

Background: Protein profiling with high-throughput sample preparation and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis is a new potential tool for diagnosis of human diseases. However, analytical reproducibility is a significant challenge in MALDI protein profiling. This minireview summarizes studies of reproducibility of MALDI protein profiling and current approaches to improve its analytical performance.

Methods: The PubMed database was searched using combinations of the following search terms: MALDI, SELDI, reproducibility, variation, precision, peak intensity, quantification, peptide, biomarkers, and proteomics. Retrieved articles meeting acceptance criteria were detailed reports on the reproducibility with MALDI protein profiling and studies describing efforts to improve the analytical performance with this technology.

Results: The reported intraexperiment CVs of the peak intensity vary highly between individual protein peaks, with the reported mean CV of the peak intensity varying among studies from 4% to 26%. There is additional interexperiment variation in peak intensity. Current approaches to improve the analytical performance of MALDI protein profiling include automated sample processing, extensive prefractionation strategies, immunocapture, prestructured target surfaces, standardized matrix (co)crystallization, improved MALDI-TOF MS instrument components, internal standard peptides, quality-control samples, replicate measurements, and algorithms for normalization and peak detection.

Conclusions: Further evaluation and optimization of MALDI-TOF MS are recommended before use in routine analysis.