We Presented at the 69th AACC Annual Scientific Meeting and Clinical Lab Expo.
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"Applied Proteomics was formed with the goal of changing the world. That is why we are here. We want to do things big and we want to make an impact on the way we care for patients."


2005 – 2006

Origin story

Company co-founders Dr. David Agus, an oncologist, and pioneer in molecular medicine, and Dr. Danny Hillis, a leader in systems engineering and computer science, came together thanks to a series of phone calls from a mutual friend.

While their work was very different, they were both asking the same question: Why aren’t we further along in fighting disease?

Dr. Agus saw the proteome as a rich source for information, but the tools to measure proteins reproducibly did not exist. Dr. Hillis brought a new perspective and quickly realized this was an area where his expertise could make a difference.

Together, the duo introduced a novel approach to unlocking the proteome.

Dr. David Agus, MD

Dr. Danny Hillis, PhD


Change the world

In June, API was officially formed. We shared space with Dr. Hillis' Applied Minds in Glendale, CA. Our first two employees, Bruce E. Wilcox, PhD, a leading mass spectrometry scientist, and Dan Ruderman, PhD, a data analysis expert, had one imperative: change the world.

Measure everything

A foundational principle at API is the power of combinations. Measuring single proteins yielded minimal usable information. Measuring thousands of proteins reproducibly and seeing how they relate can lead to real progress. The question is: how?


Build the Linus™ platform

Mass spectrometry would be the heart of Linus, our protein discovery and test delivery engine. Alone, the “mass spec” was just a box. Every tool and process upstream and downstream had to be engineered, tested and monitored in real time.

Break stuff

We acquired the platform's building blocks and pushed each piece to its limits, taking them apart and re-engineering them in new ways. The result was the most advanced platform for protein discovery and test delivery ever created.


Prove the platform

The market crashed and discovery took a back seat to showing how to apply our platform to a particular indication. We put our team and Linus to the test. Our first target, polycystic ovarian syndrome.

2010 - 2011

Pilot studies

Recognizing the potential of the platform, well-regarded venture capitalist Jim Blair, PhD, of Domain Ventures, assisted us with two additional pilot studies targeting appendicitis and colon polyps. Both pilots yielded promising results. The colon polyps study paved the way for future work on colorectal cancer and eventually led to the SimpliPro Colon™ test.


The business of saving lives

We were laser-focused on developing a product. Colon polyps and colorectal cancer were prime areas to address given the clinical need, sample availability and lack of compliance with current testing methods.

New HQ: San Diego

Things were getting cramped in Glendale. It was time for us to find a new home. We relocated to biotech beach, San Diego. Why? Have you been here?


Parallel thinking

A product was on the way. We began building our CLIA lab while conducting R&D on the yet-to-be-defined product. By taking parallel paths, we reduced time-to-market by a full year.

CLIA Lab Certification

The largest assay ever

In just eight weeks, our team deployed Linus on colon cancer. The resulting assay was the most effective mass spectrometry assay ever developed:

  • Measured 187 proteins simultaneously
  • Processed 274 patients in a balanced case-control study, the largest such study ever conducted


We've got something here

The data from Linus resulted in viable colorectal cancer classifiers. A product was within reach. The remainder of the year focused on validating these classifiers and preparing for product development.

CAP Accreditation

Hvidovre Hospital collaboration

We started a close collaboration with Prof. Hans Jørgen Nielsen of Hvidovre Hospital in Copenhagen and gained access to the high-quality colorectal cancer sample sets that helped with the development of the SimpliPro Colon test.


Ramp up

Product development was in high gear. We built a robust infrastructure to support the upcoming launch and rigorously tested classifiers. Our goal was to launch our product by the end of the year.

Signature identified

In September, we finalized the 11-protein signature for our first product. We had four months to launch the product.

The SimpliPro Colon test

What was considered impossible less than a decade earlier became a reality: On December 17th, we made the SimpliPro Colon test available to physicians throughout the U.S. It was the first blood test to assess risk of colorectal cancer and advanced adenoma in symptomatic patients utilizing a multi-protein analysis platform.


Success in the market

The SimpliPro Colon test gained tremendous support in its first year. With industry-leading turnaround times and the convenience of a mobile phlebotomy option, we saw steady growth in test orders and numbers of ordering physicians.

Continued progress

With a successful product launch, our work continued as we:

  • Published two manuscripts supporting the SimpliPro Colon test
  • Launched and completed the first of several planned IRB-approved clinical utility studies
  • Filed several patent applications supporting the SimpliPro Colon test and Linus

Never stop innovating

We’re utilizing dried blood spot technology to help realize our vision of a world where people can access valuable information about their health, cost effectively and on a regular basis. To date we have:

  • Laid the groundwork for using dried blood spot technology to deliver the next-generation of the SimpliPro Colon test
  • Studied the use of dried blood spot in other areas of interest


Staying true to the vision

The SimpliPro Colon test was just the beginning. We continue to work on the next phase of transforming healthcare through proteomics.