March 2017 - Vol 9, Issue 1
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Product News: What’s New?

Elements for Metabolomics Version 1.3

Elements 1.3 is faster and more responsive, capable of handling a thousand or more raw files with the same ease of use and intuitive interface that has made Scaffold an industry standard. This version introduces a number of exciting new features, including:

Scaffold perSPECtives Version 2.1

Scaffold perSPECtives is the tool you need to analyze today’s larger, more complex proteomics experiments. It supports complicated experimental designs, properly accounting for fractionation and technical and biological replicates, and it allows you to categorize samples by various traits or subject characteristics to help you explore the relationships in your data.

Used in conjunction with Scaffold, perSPECtives enables you to take your proteomics analysis to the next level. Hundreds of search engine results files may be loaded into Scaffold in smaller batches, filtered and exported as mzIdentML files, which can then be combined in perSPECtives and organized and analyzed as a large-scale study. mzIdentML files created by search engines (including Mascot and PEAKS) can be loaded directly into Scaffold perSPECtives, as well. Its powerful statistical and visual tools elicit the biological significance of trends in your data.

Scaffold perSPECtives 2.1 offers a number of powerful new features, including:

We encourage you to evaluate the newest versions of our products. To arrange a web demo, please contact or visit our website for a trial.

Product News: Coming Soon

New releases of Scaffold Batch and Scaffold PTM are in the works, as well. In particular, the new Scaffold Batch will include a graphical user interface (GUI) for improved usability and enhanced support large data sets.

Check our website and future newsletters to receive the most up to date information about all of our products.

Upcoming Conferences

Proteome Software at US HUPO

US HUPO will take place this year from March 19th through the 22nd in San Diego, California and our own Philip Seitzer will present a poster highlighting the powerful summarization hierarchy experiment organization approach and statistical framework available in Scaffold perSPECtives and Elements for Metabolomics.

Proteome Software at ASMS 2017

Please join us at this years ASMS conference in Indianapolis, IN from June 4th through June 8th. Our users group meeting will take place on Sunday June 4th at 3:00 PM at the Hyatt Regency in Studio One (3rd floor).

For more information and to register, click here .

We can also be found at both #218 in the exhibition hall for the duration of the conference with more details to come. Information about ASMS this year can be found at .

Do you have a publication that cites Scaffold or Elements? Let us know! We will post a citation about your publication on our website and spread the word about your great work. Send us an email to with the details.

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