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Agilent Technologies’ Spectrum Mill Searches Now Supported in Proteome Software’s Scaffold 2.1


Agilent Technologies and Proteome Software today announced that Proteome’s Scaffold 2.1 software now supports the processing of search results from Agilent’s Spectrum Mill protein database search engine.

Scaffold statistically validates peptides and proteins from tandem mass spectrometry data, combines results from multiple search engines and graphically displays identifications in biologically relevant formats. Spectrum Mill performs high-throughput protein database searches of MS and MS/MS data.

Researchers who load Spectrum Mill data files into Scaffold can now compare Spectrum Mill results with those of Mascot, SEQUEST, Phenyx, OMSSA and X!Tandem search engines.

“By supporting the Spectrum Mill search engine, Scaffold has added another excellent tool to its arsenal, making it even easier for researchers to combine, compare, and share MS/MS search results,” noted Christopher Mason, staff scientist at Proteome Software.

“Combining search engine data yields a far better result than would be obtained with any one search engine,” said Dr. Alex Apffel, Agilent Laboratories researcher. “Users can ’rescue’ spectra that would otherwise be rejected and provide an objective statistical basis for evaluation of results.”

Agilent Laboratories, the company’s central research organization, collaborated with Proteome Software to help researchers achieve higher-quality data through the integration of Spectrum Mill and Scaffold. The new version of Spectrum Mill for MassHunter Workstation offers a number of unique capabilities:

* Accepts data from most mass spectrometric instruments;
* Is one of a few programs that exploit high mass accuracy data in MS and MS/MS spectra for improved specificity and confidence in search results;
* Allows easy identification of unexpected protein modifications; and
* Offers superior visualization tools to aid in automatic and manual validation, inspection of search results and display of differential expression.

To download Scaffold 2.1, please visit


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