July 2017 - Vol 9, Issue 3
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Proteome Software Summer Newsletter

With another year’s ASMS over, it is time for an update from Proteome Software. Thank you to all who attended our User Group meeting or stopped by our booth. The conference this year was exhausting, informative, fun and we got a lot of great feedback from our users that we hope to incorporate into future releases.

Scaffold DIA Announced

For all who could not make it to the Users Group meeting we premiered and gave a live demo of our new product, currently slated for release by the end of this year, Scaffold DIA! Proteome Software strives to keep up with current and future trends in proteomics and we plan to stay ahead of the curve with the introduction of a spectral library search program for data independent acquisition proteomics. As with all of our software users can expect a simple, easy to use interface, numerous options for collaboration such as reports and sharable files and robust statistical analysis built right in. If you are interested, please send a message to sales@proteomesoftware.com to be included in updates about the program.

What’s New in Proteomics?

There are big developments in current products as well. The release of Scaffold 4.8.2 includes the new Batch Wizard. This feature allows users to create and run Scaffold Batch using an easy to use wizard - no more editing XML files! Simply fill out a few fields and let the Batch Wizard process multiple Scaffold jobs without any additional input. Scaffold Batch requires a Batch key; if you are interested please contact sales. Proteome Software is offering a promotional price on Scaffold Batch until the end of the year.

New versions of Scaffold PTM and Scaffold perSPECtives were also released just prior to ASMS 2017. Scaffold PTM now displays ratios of modified to unmodified spectra and has a new and improved Proteins View. Scaffold perSPECtives has new quantitative features, including a volcano plot and quantitative scatterplots, as well as Principal Component Analysis.

What’s New in Metabolomics?

Finally, in metabolomics, the NIST 2017 spectral library (Edit > Library Manager > Download Libraries) was released recently and is available for Elements users now from our website. With over 14,000 compounds the new library is significantly larger than the 2014 version. Elements has seen many improvements including the ability to create personal spectral libraries and built-in PCA along with performance improvements. If you have previously evaluated Elements we encourage you to try out the new version and see the dramatic improvements in action in your laboratory. If you have not, now is the time! All inquiries can be addressed to sales@proteomesoftware.com. Proteome Software is also offering a promotional price on Elements until the end of the year.

Please visit our website to request a free evaluation of any our products or to open a support ticket. Our new knowledge base, found here:


contains a wealth of information including FAQs, product documentation, white papers, a presentation archive and more! As always, if you have a recent publication that references any of our products please contact us; we will add you to our list of publications.

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 sales@proteomesoftware.com with the details.

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