BCNP Consultants European Chemistry Partnering 2017 Ffm Germany 600x60px
Document › Details

Agilent Technologies Inc.. (8/6/08). "Press Release: Agilent Technologies’ Spectrum Mill Searches now Supported in Proteome Software’s Scaffold 2.1". Santa Clara, CA & Portland, OR.

Organisation Organisation Proteome Software Inc.
Products Product SpectrumMill proteomics workbench
  Product 2 Scaffold proteomics meta-analysis software
Person Person Endicott, Eric (Illumina 201310– Director Global Public Relations before Agilent 201204 Global PR Manager)

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

About Agilent's Spectrum Mill

Spectrum Mill for MassHunter Workstation from Agilent Technologies provides rapid (~200 msec/spectrum) turnaround even for complex queries. It quickly identifies proteins and peptides via fast database searches, unique algorithms, intelligent parallelization and iterative search processes. Spectrum Mill can operate in identity mode to find unmodified peptides, or in variable modifications or homology mode to look for post-translational modifications, mutations, and chemical modifications. It also offers de novo spectral interpretation for peptides not found in any database. Spectrum Mill software can identify relative abundance differences of twofold or greater without complicated isotope labeling, but also supports all common labeling techniques.

About Proteome Software

Scaffold 2.1 Software is the industry-standard MS/MS meta-analysis tool that displays a complete, experiment-wide view of the proteins identified in a tandem mass spectrometry experiment. Scaffold helps proteomics researchers validate, visualize, and share their data. More information about Scaffold 2.1 is available on the web at

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 19,000 employees serve customers in more than 110 countries. Agilent had net revenues of $5.4 billion in fiscal 2007. Information about Agilent is available on the Web at

# # #


Eric Endicott
Agilent Technologies
+1 408 553 2005

Christopher Mason
Proteome Software
+1 503 244 6027

Record changed: 2016-03-19


Picture Fairtec GmbH Worldwide Event Solutions 600x60px

More documents for Agilent (Group)

To subscribe to our free, monthly mass spectrometry newsletter, please send an e-mail to and simply fill the subject line with the word »MSC newsletter«

To get even more information, please take a look at our [gs] professional services offering and read the gene-sensor Product Flyer [PDF file]

Please visit also our web portals for the Eurpean life sciences and the life sciences in German-speaking Europe (DE, AT & CH) at and


Picture EBD Group BIO-Europe Spring 2017 BES Barcelona Spain March 600x60px

» top


Picture [iito] Twitter iitoLifeScience Life Sciences Mass Spec 120x120px BCNP Consultants European Chemistry Partnering 2017 Ffm Germany 120x180px Picture EBD Group BIO-Europe Spring 2017 BES Barcelona Spain March 120x180px Picture AB Sciex Berliner LCMSMS Symposium 2017 Right 120x80px Picture [LSE] – The Business Web Portal 120x600px Banner Fairtec GmbH Solutions for Smarter Business Events Exhibitions 120x120px Picture [iito] Twitter iitoLifeScience Life Sciences Mass Spec 120x120px