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As Competition Heats Up for New Quantitation Software for Labeled and Label-Free Experiments

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SEATTLE — New quantitation software packages for analyzing both labeled and label-free experiments were big on the menu at the American Society for Mass Spectrometry conference, held here this week.

"Quantitation is a major drumbeat," said David Hicks, senior director of proteomics and mass spectrometry at Applied Biosystems. "There's a new population of clinicians entering in to do biomarker research. Aside from their investment in mass specs, they also need reagents and software to complement their mass spec."

ABI in January launched its Protein Pilot software for protein identification and quantitative analysis of iTRAQ, ICAT, and SILAC experiments. The software uses the Paragon search engine for protein identification and can use the Mascot search engine.

Thermo Electron launched here this week its SIEVE software designed to do label-free differential expression analysis. The technology offers an automated workflow to compare LC/MS analyses from large sample populations, and is a "highly accurate" tool for analyzing data from biomarker discovery experiments, Thermo officials said.

Ken Miller, proteomics product marketing manager at Thermo, said that Thermo scientists used SIEVE to analyze the Association of Biomolecular Research Facilities' Proteomics Research Group protein mixtures.


"I was surprised about the label-free [mass spec methods] — how well they did."

At ASMS, Thermo officials noted that a study on relative protein quantitation by the ABRF's PRG (see ProteoMonitor 2/16/2006) found that label-free mass spec methods performed relatively well in determining the relative quantitations of two unknown protein mixtures, compared to other methods, such as Coomassie and silver stained gels.

"I was surprised about the label-free [mass spec methods] — how well they did," said Chris Turck, the chair of the PRG after he presented results of the study at the ABRF meeting in February. "Based on these results, I would look into the label-free methods."

Thermo this week also launched an updated version of its BioWorks protein identification and quantitation software. The new BioWorks version 3.3 handles major quantitative labeling techniques, including iTRAQ, SILAC, and ICAT, as well as label-free quantitation. It uses Thermo's Sequest algorithm for the identification of peptides and proteins. Users can also import Mascot results after a Sequest search has been run.

Bruker officials said that the company's ICPL labeling kit also performed well in the ABRF's PRG study.

"Bruker received the top score in the PRG protein quantitation study," said Michael Schubert, executive vice president of Bruker Daltonics, pointing to the first row of a table of ABRF results. He said the company used its ICPL duplex kit and its Warp-LC 1.1 software.

Launched this week, the Warp-LC 1.1 software is designed to analyze quantitative proteomic experiments using ICPL, SILAC, iTRAQ, and 18O/16O-C terminus labeling.

Meantime, Agilent launched this week its GeneSpring MS software that allows researchers to import, store, and visualize GC/MS and LC/MS data from large sample sets, and to detect changes in the profile of proteins, peptides, and metabolites across many samples.

"GeneSpring MS accelerates biomarker discovery by allowing researchers to profile proteins or small molecules associated with changes in cellular function," said Francois Mandeville, manager of informatics solutions at Agilent.

New ICPL, iTRAQ Reagents

In addition to new quantitation software, Bruker launched a new triplex version of its ICPL quantitative labeling reagent that enables researchers to label three samples at once, while ABI promised to launch a new 8-plex version of its iTRAQ reagent that allows researchers to label up to eight samples at once.

"For the first time, three entire proteomes can be analyzed [using ICPL Triplex] quantitatively, simultaneously, and using robust statistics, cutting down on protein pre-fractionation efforts significantly," said Detlev Suckau, head of proteomics development at Bruker Daltonik in Germany.

While ABI has not yet launched its 8-plex iTRAQ, Darryl Pappin, a principal scientist at ABI, gave a presentation here this week showing the results of cell cycle experiments that pioneered the use of such a reagent.

"You can analyze up to eight samples in a single run," said Hicks. "That's invaluable in a time-course study. … You're not just doing identification, you're doing the quantification and how they relatively compare quantitatively."

Hicks said the 8-plex iTRAQ is currently in the development and manufacturing stage at ABI. The product may be released later this year, he said.

— Tien-Shun Lee ([email protected])

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