MS1-based, label free quantitation: PASS Suite employs a version of SuperHirn, a program developed in the Aebersold laboratory at ETH Zurich, to perform MS1-based, label free quantitaiton. (The original developer of the program, Dr. Lukas Mueller, has been working with Integrated Analysis since 2009 and formally joined Integrated Analysis as the Senior Consultant in the Bioinformatics group.)  The program runs on an architecture based on cloud-computing so that quantitation can be performed rapidly  on dozens or hundreds of MS files. SuperHirn is seamlessly integrated with PASS Suite, has prebuilt graphics and reports, and can even increase the number of identified peptides and proteins by aligning and matching spectra from different MS runs. To learn more, you may either obtain the poster and/or brochure, or schedule a demonstration that will quickly explain how our solution fits your needs.

Protein redundancy removal: The degree of protein redundancy (i.e., highly homologous protein in the final resulting data sets) is a problem in proteomics, even if peptide/protein searches are run against supposedly non-redundant FASTA files. If there are redundant proteins in the data, it is not possible to provide accurate biomarker reports because protein count information may be split between multiple, highly homologous proteins that appear as separate, distinct proteins.  Integrated Analysis has developed a novel approach to provide fully user-controlled protein redundancy removal so that the biomarker reports provide accurate information, particularly with respect to accurate quantitation information.

To learn more how Integrated Analysis addresses the protein redundancy problem, please download the US HUPO 2010 poster, get the PASS brochure, or schedule a customized demonstration.

Capability to handle datasets as large as terabytes : Today's mass spectrometers are generating ever more data. Many of the original data management solutions were never designed to handle large amounts data and therefore run extremely slowly or, in many cases, simply crash. Integrated Analysis has always built large data warehouses for some of the largest data-hungry consumers, such as Sun Microsystems, Oracle, the Baltimore Sun, and National Institutes of Health. We have designed our proteomics data warehouse, PASS, to handle dozens, hundreds, or thousands of MS files (i.e., terabytes worth of raw data). Researchers can query their data and get specific, customized reports within seconds. To learn more, please download the PASS brochure or schedule a customized demo of the "Johns Hopkins" dataset, which includes data aggregated from over 6 clinically-oriented biomarker projects, which consist of over 5,000 MS files and growing....

Secure and robust storage of terabytes of data: The raw data files generated by a laboratory represent valuable, sensitive information—its intellectual property. A laboratory needs a system which can guarantee safe, secure, and robust storage of this sensitive data. Integrated Analysis' DASH product can store a few gigabtyes to tens-of-terabytes worth of data in a secure, robust manner designed for21 CFR Part 11 compliance. To learn more, please contact us at This e-mail address is being protected from spambots. You need JavaScript enabled to view it or +1.301.760.3077.

Interactive reporting and querying to identify biomarkers: Many software products claim that they provide users with customized queries and reports. But PASS truly shines in this area.

To truly empower researchers with the ability to query  data, a software system needs to be flexible in its reporting interface.  PASS gives researchers an easy, and extremely flexible querying interface that doesn’t require any knowledge of the programming language. Moreover, the customized queries and reports return data within seconds, even against terabytes of data. A live demonstration of these features against a dataset of thousands of MS files will highlight PASS’s advantages compared to the competition.

Ease of use, yet powerful capabilities: From the beginning, we focused on two goals with PASS’s design. The first was to provide a software package capable of handling up to tens of terabytes worth of data (see above); the second was to keep the system as easy to use as possible, but  still provide advanced capabilities. We believe that we have achieved this second goal by first integrating all the different bioinformatic processes, such as searching, quantitating, and reporting, and then by providing a host of prebuilt, fully-documented template reports. Please schedule a live demonstration of our solution and let us show you how easy it is to analyze all of your proteomics data.

Cloud-based and/or cluster-based architecture for massively parallel execution of searches and/or other bioinformatics algorithms: Real-time processing is becoming more and more important to gain (or maintain) a competitive edge. The faster files can be searched and processed, the sooner researchers can start analyzing their data.  This is particularly true as modern mass spectrometers are generating larger files that take longer to search and process. Sample sizes are increasing per project and fractionation of the samples is increasing the overall number of MS files generated. The whole process is becoming more high-throughput.

Integrated Analysis's cloud-based and cluster-based software architectures automatically allow all your bioinformatics algorithms (search programs, quantitation programs, statistical programs etc.) to run on a cloud-computing and  cluster-computing based platform. Dozens or even hundreds of computer nodes are running the algorithms in parallel. With our PASS software, it doesn’t even cost much more than running the algorithms on a single computer! Download our PASS brochure to learn more, or contact us for a one-on-one demonstration.

Customizability of solution and ability to partner with laboratories: Our clients don't want products. They want solutions. Integrated Analysis was founded in 2002 as a consulting company and still boasts a strong consulting culture. Clients, say they most like the speed and willingness with which we customize the solution to meet their unique needs so they have the infrastructure, tools, and services needed to successfully analyzie and interpret their data. We want show you examples of what we have done for our clients so please call us at +1.301.760.3077 or email us This e-mail address is being protected from spambots. You need JavaScript enabled to view it or request a demonstration via our document request form.