Bioprocesses for therapeutic protein production typically require significant resources to be invested in their development. Underlying these efforts are analytical methods, which must be fit for the purpose of monitoring product and contaminants in the process. It is highly desirable, especially in early-phase development when material and established analytical methods are limiting, to be able to determine what happens to the product and impurities at each process step with small sample volumes in a rapid and readily peiformed manner. This study evaluates the utility of surface-enhanced laser desorption ionization mass spectroscopy (SELDI-MS), known for its rapid analysis and minimal sample volumes, as an analytical process development tool. In-process samples from an E. coli process for apolipoprotein A-IM (ApoA-IM) manufacture were used along with traditional analytical methods such as HPLC to check the SELDI-MS results. ApoA-IM is a naturally occurring variant of ApoA-1 that appears to confer protection against cardiovascular disease to those that carry the mutated gene. The results show that, unlike many other analytical methods, SELDI-MS can handle early process samples that contain complex mixtures of biological molecules with limited sample pretreatment and thereby provide meaninful process-relevant information. At present, this technique seems most suited to early-phase development particularly when methods for traditional analytical approaches are still being established. (C) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 26: 881-887, 2010