Process development for biologics is expensive and lengthy, tools are needed to rapidly understand where the difficulties will lie, and, hence, rationally deploy resources. In this work we introduce and evaluate a methodology to determine the manufacturability of a protein candidate. The methodology determines protein impurities by mass spectrometry and separation difficulty from the product based on adsorption properties deduced from a single set of experiments. This information can aid early process strategy decisions to target hard to remove protein impurities (nearest neighbors) and allow the re-evaluation of conventional process synthesis. The methodology chosen gives consideration to the fact that at this point in early phase development, material, and established analytical methods are limiting. This study uses surface enhanced laser desorption ionization mass spectroscopy (SELDI-MS), for its rapid analysis and minimal sample requirement to measure product and contaminant adsorption properties. The technique is used to provide an array of hydrophobic and electrostatic conditions for protein adsorption. The adsorption pattern produced for each protein is analyzed and visualized via a star plot. Dendrograms then define nearest neighbor protein contaminants by quantifying differences in the adsorption pattern between the product and contaminants. By comparison to an existing process to manufacture a 28 kDa recombinant protein expressed in Escherichia coli, we confirm the method is capable of determining where the greatest separation difficulty lies and what separation methods should be considered. The technique identified that the nearest neighbor contaminants were product-related proteins (28.6 and 29.1 kDa/e). Thus demonstrating a capability to measure the relative difficulty of purifying early stage protein candidates where little is known about the separation properties of products and contaminants, or the process sequence for their production. Biotechnol. Bioeng. 2011;108: 1862-1871. (C) 2011 Wiley Periodicals, Inc.