Proteome Software Newsletter
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March 2015 - Vol 7, Issue 1
Come visit us at these upcoming conferences
ABRF Booth #228. St Louis MO, March 28-31, ABRF web site
MSACL Booth #19. San Diego CA, March 28-31, MSACL web site
ASMS Booth #31. St Louis MO, May 31-June 4, ASMS web site
ASMS User’s Group will be held on Sunday afternoon, May 31. Sign up here.
New Scaffold Features
Since the Scaffold 4.3.3 release we have added these features:
- Support for new input file formats including AB SCIEX Protein Pilot 5.0 files and mzXML files from Agilent Spectrum Mill.
- Scaffold now also provides precursor intensity quantitation for searches performed on MGF files exported from Waters Progenesis QI for Proteomics
- Improved statistical analysis with multiple comparison corrections and the ability to specify a significance threshold.
- Quantitation with iBAQ.
- An enhanced Quantify View, including a Volcano Plot, a Venn Diagram display based on relative quantitation, an improved Quantitative Scatterplot and coordinated protein selection throughout the View.
New perSPECtives features
A variety of new features have also been added to perSPECtives, including:
- Precursor intensity quantitation.
- Log2 fold change as a display option.
- The ability to filter on p-value.
- New exports and right-click options.
- A new Visualize View containing a true interactive heat map with dendrograms.
- FDR thresholding and protein grouping during loading performed according to user-defined parameters.
Check out Elements for Metabolomics!
Elements for Metabolomics, our newest tool for processing, organizing and interpreting large scale metabolomics experiments is in beta testing.
Elements employs parallel processing to efficiently analyze hundreds of MS samples with or without MS/MS spectra. Metabolites are identified using multidimensional search and scoring algorithms. Search with the NIST and HMDB spectral libraries, or import your own.
Backed by robust and cutting edge non-parametric statistical models to normalize and interpret data, Elements includes proper handling of biological and technical replicates. Share results with a free viewer.
Come see a demo!
Do you have a publication that cites Scaffold? Let us know!
We’ll post it on our website and spread the word about your great work. Send us an email with the details.
New Tutorial Videos
Exploring the Samples View
Quantitation with Q+
Popular White Papers
Precursor Intensity Quantitation in Scaffold (2014)
Scaffold Protein Grouping and Clustering (2014)
Configuring Proteome Discoverer 1.3 and 1.4 for optimal performance in Scaffold 4 (2014)
In other news...
If you have any questions about Proteome Software or our products, contact us here.
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