Alliance Protein Laboratories is a contract research firm specializing in biophysical analysis. We offer:



APL is a spin-off from the Protein Chemistry department at Amgen. It was founded in 1998 by Drs. Tsutomu Arakawa and John Philo. Our laboratory is located in the heart of the biotechnology cluster in San Diego, CA. Our clients include over 400 companies in North America, Europe, Asia, and Australia as well as major universities and non-profit institutes. In July of 2017 APL became a division of KBI Biopharma.



Tsutomu Arakawa, Ph.D.

Vice President, R&D


Before co-founding APL in 1998 Tsutomu spent over 14 years in Protein Chemistry at Amgen as Research Scientist and Lab Head. His group was responsible for protein purification and characterization for discovery research and pre-formulation studies. While there he purified dozens of recombinant proteins and characterized their structure...

N. Karl Maluf, Ph.D.

Senior Scientist


Before joining APL in 2013 Karl was an Assistant Professor in the Department of Pharmaceutical Sciences at University of Colorado Denver for 6 years, where he studied virus assembly and DNA-protein interactions via AUC, fluorescence, stopped-flow kinetics, and other biophysical, biochemical, and thermodynamic approaches...

John Philo, Ph.D.

Vice President, R&D


Before co-founding APL in 1998 John spent over 6 years in Protein Chemistry at Amgen, where his primary responsibilities were protein characterization using analytical ultracentrifugation, light scattering, and calorimetry. While there he pioneered new sedimentation velocity techniques appropriate for biotechnology products...

Huimin (Cynthia) Li, M.S.

Principal Scientist


Before joining APL in 2018 Cynthia spent almost 23 years at Amgen. During the 23 years at Amgen, she managed and executed numerous bioanalytical testing projects for molecule assessment of therapeutic protein candidates, protein high-order structure characterization, product comparability and similarity assessments...


  • We've been doing this for over 18 years and have completed over 2,100 projects for 400+ clients world-wide.

  • At APL the experiments and data interpretation are done by recognized experts with extensive experience in these biophysical techniques, not by a technician, and on our own equipment, not in a university lab.

  • We've already worked with over 250 biotherapeutics and vaccines, including most of the major biotech products (cytokines, interferons, growth factors, scores of monoclonal antibodies, vaccines, viral vectors for gene therapy ...) and we have already been working with biosimilars for over 13 years. That collective experience helps us interpret our data, and can help get your product to the patients who need it!



If you are even thinking about using another company for biophysical analysis see questions you need to ask a biophysical lab.

Frequently asked questions

Do you run biophysical analyses under cGMP standards?

No, and thus we cannot accept samples for analysis to meet a release specification. We of course try to conform to principles of good laboratory practice, but meeting cGMP standards for these biophysical techniques is generally not possible. The software for these instruments is not compliant with 21 CFR Part 11 guidelines, and the protocols have not been formally validated. It is our understanding that characterization data for products under development does not need to meet cGMP standards but only needs to be "suitable for purpose". Data we have generated has been used by our clients in documents submitted to regulatory agencies, such as CMC sections, comparability protocols, or responses to regulatory queries. However, it is your responsibility, not ours, to ascertain what regulatory guidelines may need to met for your intended use of the data.

Who have you worked for?

We have done work for over 350 different industrial clients in the US, Canada, Europe, Asia, and Australia, including most of the major biotechnology and pharmaceutical companies. We have also done work for a number of universities and several non-profit research organizations and government labs. Among the industrial customers we can mention are Allergan, Aventis, Baxter, Bayer, Biogen-IDEC, Chiron, Chugai, Gryphon Therapeutics, Immunex, MedImmune, Schering-Plough, Seattle Genetics, Serono International, and Zymogenetics.

Do you charge per sample, per analysis, per job, per hour, or...?

We can use any of these methods. Our fee structure depends on the nature and type of work, as well as on your preferences. CD studies are normally charged on a per sample basis; other methods are also generally per sample (usually per set of 3 samples for AUC), but may also involve setup fees. We can quote a fixed price for a set of experiments, or a rate per sample for characterization studies, or we can simply agree on a rate per hour/day/week. Purification projects are usually best handled based on time spent or price per purification step employed. The majority of the characterization projects we do cost less than $5,000 total.

For contract characterization services what sort of reports and data do you provide?

Usually we provide a summary report that outlines the methods used, gives graphs and/or tables of the results, and summarizes the conclusions, in the form of a locked Adobe Acrobat (.pdf) file. If you have specific reporting or formatting requirements those should be communicated before we agree on a price. We do not normally supply the raw data (computer files). Indeed the FDA has asked us not to do so and most clients would not have software that could read the files anyway. If you absolutely must have the raw data you would need to discuss this with us in advance.

What is your normal turn-around for analytical work?

The turn-around will likely vary depending on the techniques involved. Typically for CD studies we are able to begin work on a new project within 1-2 weeks. Recently for AUC or light scattering studies turn-around to a completed report has been 2-4 weeks. We work strictly on a first-in, first-out system, based on when the samples actually reach us. We do not accept "rush" jobs at higher fees because this can effectively lock out smaller companies.

Will you provide services to universities or non-profit institutions at reduced fees?

We welcome collaborative research projects with academic investigators, and will generally do such work at a considerably reduced fee. In some cases we seek only to recover our costs for materials and consumables. Obviously the time we have available for such projects is very limited. Our full-fee paying clients get top priority, and reduced-fee work generally must wait for slack periods (which are very few).

Can you express my protein as well as purify it?

Sorry no, we are not equipped to do the expression ourselves.

How do you maintain confidentiality?

For our industrial clients we normally execute a Non-Disclosure Agreement (NDA) or a Materials Transfer Agreement (MTA), either at some point during pre-contract discussions or as part of a contract or service agreement. At the conclusion of the work any left-over samples are usually destroyed, but upon request they will be returned (at the client's expense).

Does your company have any financial or other ties to Amgen that might compromise confidentiality?

No, we have no ties to or formal relationships with Amgen since leaving our employment there over 15 years ago. Our sole business connection to Amgen is that Amgen has been an occasional client, representing less than 1% of our total business.

Do you have a sample submission form?

Yes. It's available on our Contact Us Page