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Agilent Technologies introduces powerful application software for new LC/MS portfolio


Programs increase productivity, throughput of mass profiling, protein research, metabolomics

ORLANDO, Fla., PITTCON 2006, March 13, 2006, Agilent Technologies Inc. (NYSE: A) today introduced powerful application software for its 6000 Series portfolio of liquid chromatograph/mass spectrometer (LC/MS) systems, which is expected to double Agilent’s market share in LC/MS by 2008. The Agilent MassHunter Profiling software, Agilent MassHunter Bioconfirmation software, and upgraded Agilent Spectrum Mill for MassHunter Workstation improve the productivity and throughput of diverse molecular profiling applications, protein identification and quantitation, peptide/protein confirmation and characterization, and metabolomics.

“Customers want valid answers to complex questions with high reproducibility in less time than it takes them today,” said Rick Carberry, LC/MS senior director of Marketing. “Starting with superior experiment result data from Agilent’s industry-leading sample prep, separations and LC/MS products, these application software packages produce consistently better insights much faster.”

MassHunter Profiling Software

Mass profiling uses MS data to reveal relevant differences between samples in order to flag these differences for further analysis and identification with MS/MS. Scientists use mass profiling to compare the expression of peptides, proteins or metabolites for biomarker discovery in different samples (e.g., healthy versus diseased cells or plasma); to detect pharmaceutical impurities; or to analyze samples for targeted compounds such as pesticides or narcotics.

The Agilent 6210 TOF and new 6410 Triple Quadrupole LC/MS and 6510 Q-TOF systems employ unique, intelligent algorithms that can identify all the detectable components or molecular features in accurate mass LC/MS data, in even very complex mixtures. These algorithms generate feature lists that include retention time, neutral mass and abundance data, where all of the related ions of a molecular feature are grouped together (isotopes, charge states, adducts and multimers). This affords a significant reduction in complexity of the original raw data set, facilitating comparative analysis. Based on these lists, the MassHunter Profiling software can:

Align, normalize and statistically assess molecular features in a single group.
Statistically compare composite molecular feature sets from two different groups.
Visualize and identify statistically significant feature differences between the groups.
Provide detailed inspection of the data for a select feature across all samples.
Comparisons between three or more sample groups are possible via an export to the GeneSpring bioinformatics platform, where a variety of statistical techniques are available for analysis and classification.

MassHunter Bioconfirmation Software

Agilent MassHunter Bioconfirmation software is ideally suited for scientists involved in recombinant protein expression, known protein characterization, or synthetic peptide confirmation. When coupled with the Agilent 6210 Time-of-Flight LC/MS, the software helps to confirm identities and identify variants before expensive testing begins.

The MassHunter Bioconfirmation software uses sophisticated algorithmic tools to generate superior and accurate lists of peptide mass, retention time and abundance. This improves productivity and throughput by allowing truly automated and interactive confirmation and characterization of recombinant proteins or synthetic peptides.

The software comprises three main components that provide:

Interactive software for deconvolution and confirmation of intact proteins.
Protein sequence editor/matcher for protein or peptide characterization.
Automated batch processing and confirmation reporting “on the fly.”
For both electrospray-TOF and MALDI-TOF data, mass lists can be imported into a database search program, such as Agilent Spectrum Mill for MassHunter Workstation, for fast identification by peptide mass fingerprinting.

Spectrum Mill for MassHunter Workstation

Agilent Spectrum Mill for MassHunter Workstation is designed to facilitate high-throughput proteomics and biomarker research. The Spectrum Mill software allows users to compare large data sets across multiple experiments and summarize results at the protein level. Through enhanced MS/MS spectral-quality filtering and iterative database searching, the software can increase the speed of protein identification and quantitation ten-fold. The software can reveal two-fold or greater changes in relative abundance without the need for labeling. When more precise quantitation is needed, the Spectrum Mill software now supports a wide variety of stable isotope-based labeling strategies -- a unique offering.

Other new features of the upgraded software designed to improve productivity and facilitate individual customer workflows include:

Support for custom user-configurable post-translational modifications (PTM) or amino acid modifications for PTM studies or biomarker discovery.
Improved autovalidation of database search results, including automated reversed database matching, Rank1-Rank2 scoring and proton mobility scoring, to find more valid peptide hits without manual review.
“De novo” spectral interpretation tools for proteins not found in any database.
Intelligent spectral merging that only merges scans from the same mass precursor within a specified mass and time window if the MS/MS spectra are similar.
Support for neutral loss triggered MS3 or pseudo-MSn scan capabilities of Agilent ion trap systems to facilitate phosphoproteomics studies.
The ability to compare data generated within or across a study or across multiple instrument platforms, with flexible results reviews at the peptide and protein levels. Add-on modules are available that allow the software to process non-Agilent data formats.
For more information about the application software suite, visit

Agilent in Mass Spectrometry

Agilent is a leading provider of GC/MS, LC/MS and ICP-MS technologies for organic and inorganic spectroscopy. Among the company’s key products are the 5973 and 5975 inert MSDs, the 7500 Series ICP-MS systems, and the new Agilent 6000 Series LC/MS triple quadrupole, ion trap, time-of-flight and quadrupole time-of-flight instruments. Agilent provides innovative HPLC-Chip/MS technology and the broadest range of ion sources in the industry. As a leader in separations and software, Agilent can address the entire customer workflow from sample introduction through data analysis.

About Agilent Technologies
Agilent Technologies Inc. (NYSE: A) is the world’s premier measurement company and a technology leader in communications, electronics, life sciences and chemical analysis. The company’s 20,000 employees serve customers in more than 110 countries. Agilent had net revenue of $5.1 billion in fiscal 2005. Information about Agilent is available on the Web at


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