What You Need to Know About the OneOmics Project – A Discussion with Mark Cafazzo

Sep 23, 2015 | Blogs, Life Science Research | 0 comments

I recently had the opportunity to sit down with Mark Cafazzo, Global Proteomics Market Manager, SCIEX, to discuss the SCIEX OneOmics™ Project:

Becky: I’ve heard about the OneOmics Project. Can you share more about it?

Mark: The OneOmics Project is the first cloud-based, app-enabled initiative that allows scientists to seamlessly and securely* store, process, and share multi-omics results (genomics, transcriptomics, proteomics, and more). The OneOmics Project enables researchers to integrate proteomics and transcriptomics results to obtain a deeper understanding of their biology (learn more below).

SCIEX and Illumina partnered to make the OneOmics Project possible. This partnership enables scientists using SCIEX SWATH®-based Next Generation Proteomics (NGP) applications to process, analyze, and present comprehensive quantitative proteomics data seamlessly in BaseSpace®, Illumina’s Next Generation Sequencing (NGS) cloud computing environment designed with biologists in mind. BaseSpace provides a thriving data and app ecosystem where producers of omics data can upload both NGP and NGS data and make use of a variety of apps developed by industry and academic experts to process and interpret results.

With the OneOmics Project, you can increase the speed of SWATH NGP data processing and move rapidly to a deeper multi-omics analysis. All in a single, secure environment that accelerates biological insight and discovery.

Becky: You mention the term “multi-omics”. What do you mean?

Mark: The number of ‘omics disciplines has grown tremendously over the past decade. Today this includes Genomics, Transcriptomics, Proteomics, Metabolomics, and Lipidomics to name a few. Each discipline generates vasts amount of data, with results often being interpreted in isolation.  The OneOmics Project lets researchers process their proteomics and genomics data (specifically, transcriptomics) in the same environment, enabling the development of applications that will easily integrate for deeper multi-omics analysis.  A recent study by Katy Williams (UCSF), Christie Hunter (SCIEX), and Andrew Olsen (Advaita) used the iPathwayGuide within OneOmics to help understand how placental development can go awry during certain pregnancy complications such as pre-eclampsia.

In this pilot study, researchers studied cytotrophoblast differentiation. Cytotrophoblasts are the cells that are mainly responsible for establishing an anchor between the developing embryo and placenta with the uterine wall. The researchers compared cytotrophoblasts from 2nd trimester and term placentas. SWATH proteomics data acquired using a SCIEX TripleTOF® 6600 System were analyzed in OneOmics using iPathwayGuide to identify differentially regulated proteins and their associated pathways, biological processes, and molecular functions. Then, proteomics data was compared with RNASeq transcriptomics data acquired using an Illumina HiSeq System. Both the proteomics data and transcriptomics data were correlated using the OneOmics and iPathwayGuide in the cloud. This meta-analysis allowed the researchers to discover common pathways and processes between the data sets as well as those only observed in the proteomic or transcriptomic data sets alone.

This pilot study helped to shed light on the biological significance of multiple proteins and pathways that provide an effective pipeline for converting raw data to biological answers.  Watch the complete study (10:00 min)

Becky: What do I need to use OneOmics?

Mark: If you own a SCIEX TripleTOF System or have access to TripleTOF SWATH data, you are ready to leverage the OneOmics proteomics workflow and take advantage of high-performance computing and global collaboration.

What’s more, bioinformaticians and software developers can leverage the BaseSpace environment to extend or complement existing workflows by building their own new apps—creating more scientific value.

Becky: How can I get training on OneOmics?

Mark: The OneOmics apps are designed to be simple and intuitive. Generally, users only need to upload and select the data files to process, assign study-level information, and go!

We recently introduced OneOmics Cloud Talks, videos to provide support on OneOmics and related apps in BaseSpace.  Check out the latest videos >

Users can also make use of online help within the BaseSpace application, or visit the SCIEX online community for tips and tricks and to learn from their peers. In certain situations where a more advanced tutorial is required, online videos may be accessed from within some apps and from the SCIEX website.

Becky: Are there any technical or operating requirements to set up OneOmics?

Mark: SWATH data and an internet connection are all that’s needed to begin enjoying the benefits of the OneOmics Project. While many popular browsers are supported, the SCIEX OneOmics apps are optimized for use with Google Chrome.

Becky: What can I ultimately expect to get out of the OneOmics Project?


  • Rapid biological insight into your studies, with easy to use applications
  • Faster processing of proteomics data, thanks to high-performance cloud computing
  • Share and collaborate with colleagues instantly, anywhere, anytime, using a secure cloud-computing environment
  • Integration of NGP and next-generation genomics results through working in a shared workspace

Request a demo of the OneOmics Project by commenting below. Or to learn more, please contact your SCIEX sales rep or join the SCIEX OneOmics Community.

*Cloud-based security:  The OneOmics Project is in Illumina’s BaseSpace Platform is on Amazon’s secure AWS cloud infrastructure. Download the Illumina brief to learn more about security >


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