New Software and Reagents Expand Productivity, Efficiency for Targeted Quantitative Proteomics

New software tools are being developed to address the needs of scientists in industry and academia who are seeking to quantify many specific proteins and peptides in complex biologic samples. Thousands of proteins may be present in any specific laboratory sample; however, scientists are often most willing to examine the subset of those that are typically lower in abundance and are changing in response to a disease.

Applied Biosystems (Foster City, CA, USA), an Applera Corp. (Alameda, CA, USA) business, and its joint-venture partner, MDS Analytical Technologies (Concord, Ontario, Canada), a business unit of MDS, Inc., announced the availability of a suite of integrated mass spectrometry-based solutions for conducting targeted quantitative proteomics studies. Designed for Applied Biosystems/MDS Analytical Technologies' triple quadrupole and hybrid triple quadrupole/linear ion trap mass spectrometry systems, these solutions include software packages and consumables that enable scientists to quantify proteins more effectively in biomarker research or cell biology.

Targeted mass spectrometry is emerging as a powerful tool for these quantitative assays, however major challenges remain. The need for higher-order multiplexing, improved reproducibility, and more rapid assay development for these protein panels is critical for scientists to continue to drive forward their biomarker initiatives in a streamlined, efficient way. Applied Biosystems/MDS Analytical Technologies' targeted quantitative proteomics solutions can address these challenges because they are designed to deliver consistency along with simplified, one-touch accessibility to sophisticated technology across the entire workflow.

These new tools include: mTRAQ reagents, which are chemical labeling kits for use in targeted proteomics experiments using multireaction monitoring (MRM) analysis that can be used to create global internal standards to provide an internal reference for every protein, peptide, and post-translational modification in a sample, in a simple, one-hour step. Based on proprietary Applied Biosystems technology, mTRAQ reagents are designed to improve analytic reproducibility for quantitative experiments without the need for expensive, custom, synthetic peptides.

Scheduled Multiple Reaction Monitoring is a feature that focuses instrument cycle scans for specific analytes based on the timeframe that those analytes will be entering the instrument. In proteomics, this means the instrument can scan up to 10 times more peptides with better analytic precision and yielding more information about each one. The Scheduled MRM Algorithm is part of Applied Biosystems/MDS Analytical Technologies' updated operating system, Analyst 1.5 software, which powers its mass spectrometry systems.

MRMPilot software is a new software program for use with Applied Biosystems/MDS Analytical Technologies Q TRAP systems that enable rapid development of robust MRM assays for peptides and proteins utilizing data acquired during discovery experiments. MRMPilot Software automatically builds MRM assays and utilizes the unique Midas Workflow of the Q TRAP system for more seamless and far more efficient transition from discovery to validation. These assays complement existing widely used antibody-based assays, while requiring up to 10-fold less time to develop and eliminating the need for purified proteins.

MultiQuant software is a new software package for use with Applied Biosystems/MDS Analytical Technologies mass spectrometers that processes MRM data for quantitative information. The software enables the efficient processing of many analytes and samples at the same time, with an emphasis on the requirements for processing protein/peptide quantitative workflows.

Applied Biosystems develops and markets instrument systems, software, consumables, and services for the life science market. Through a joint venture with MDS Analytical Technologies, the company is providing complete workflows for the mass spectrometry market, based on industry-leading platforms, software and new application workflows

MDS Analytical Technologies is a newly established MDS, Inc., business unit and is comprised of two main lines of business. The Sciex product range offers mass spectrometry systems through its joint ventures with two leading analytic instrumentation and life sciences companies, Applied Biosystems, a business of Applera Corp., and PerkinElmer, Inc. (Waltham, MA, USA). MDS' product range includes high-performance bioanalytic measurement systems that accelerate and improve drug discovery and other life sciences research.


Related Links:
Applied Biosystems
MDS Analytical Technologies