Proteome Software News...
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The long awaited SILAC quantitation add-on for Scaffold Q+ is here: Scaffold Q+S. See below...
Hint of the day: Click on any yellow highlighted sequence in Scaffold PTM and it will list the peptide and modifications in the PTM Sites view (upper right).
Scaffold Q+S for SILAC Quantitation
Visualize, validate and quantify SILAC-labelled, complex MS/MS proteomics experiments. Quantitate 2-plex and 3-plex (SILAC) biological samples.
View and share supporting data; check statistical probabilities; verify that statistics are valid for your data across experiments; meet journal standards.
To learn more...
Improved Statistics: Enhanced Scaffold Q+
Scaffold Q+ has been improved to include new statistical tests as well as a more robust normalization model, allowing quantitation within multi-plex samples and across groups of multi-plex samples.
Added visualization with the Mean/Median Density graph, for quick assessment of up- or down-regulation.
We Distribute HDExaminer and Progenesis LC-MSWhat is Progenesis LC-MS?
Progenesis LC-MS is a data analysis program that helps you to find and quantify the proteins showing interesting behavior in your label-free samples. It can be used for both differential protein expression and protein characterization applications.
Sierra Analytics produces a software solution for bottom-up H-D Exchange MS data analysis that provides powerful functionality to give a comprehensive picture of the deuteration uptake behavior of a protein. This information can be used to help determine protein folding behavior, protein-drug interactions, and sites of protein-protein interactions.
ASMS 2012 - Proteome Software User's Group Meeting
To sign up and RSVP for the user's group meeting in Vancouver, BC, click here:ASMS 2012 - Proteome Software User's Group Meeting RSVP
In other news. . .
Many users often ask if memory (RAM) plays a significant role in Scaffold. As an application that uses the Java Virtual Machine (JVM), Scaffold relies heavily on memory to process results and hold those results for immediate manipulation and visualization. This is why it is very important to remember to allocate your memory in the Preferences section under Edit in Scaffold.
Scaffold 3 is the industry standard in protein visualization and validation and reads the following files: Mascot (*.dat), Sequest (*.srf, *.dta/*.out, *.ms2/*.sqt), X! Tandem (*.xml), Phenyx (*.scaffold-pidres.xml), Spectrum Mill (each search result is a directory of files-load the whole directory), OMMSA (*.omx), Proteome Discoverer (*.msf), and IdentityE (*.xml, using Scaffold Plug-in from the PLGS).
Scaffold Q+S is a powerful quantitation module for analyzing SILAC multi-plex samples and supports these formats: Mascot Distiller (*.xml), Discoverer (*.msf), MaxQuant/Andromeda (Combined Results Directory)
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