The software has been continuously evolving, and the original publications can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808162/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792908/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876250/
Email firstname.lastname@example.org anytime!
Each experiment can handle a multiple samples simultaneously, limited only by the specifications of your computer. You can have Apo and six ligands all in one experiment.
Yes, we offer a free 30 day trial.
Left click and drag a box to zoom in, and drag(swipe) left anywhere in the view to zoom out. This also works for the uptake plots, and the XIC.
The “peptide set” is a list of the peptides from search output to be included in the H/D exchange experiment that we refer to as the “peptide set” which could be from nearly any output format including CSV, pepXML, Mascot, Proteome Discoverer, Bionic, XTandem, and more. The required fields for this file are sequence and charge, and optionally retention time and score. More details are provided in the peptide set import tool video in the tutorials section.
Essentially just install the software and set it as default. We have a video in our tutorials section. Also feel free to Email email@example.com and we can show you.
We currently we support Thermo and Waters high resolution instruments.
Yes. The software is able to extract what is needed accordingly.
If the mz ranges are wide, then the the peptide may have not been detected by the algorithm. If you still think it could be present, then narrow the mz ranges around the monoisotopic mz, see if it changes the XIC, and adjust the retention time around the resulting chromatographic peaks.
These are the sub range windows within which peptide peaks are expected to reside. The software only considers peak data from within these ranges to calculate the centroid. This approach can often be helpful to disregard non peak data and also provides a visual reference to confirm your peptide.
The width of these ranges is determined by the “mz / ” value in the detect panel (resolving power). HDX Workbench allows for an estimate of the linear m/z dependent resolving power exhibited by fourier transform based instruments. For example, when set to m/z ÷ 25,000, the sub range width is 0.05 at 1250 th and 0.02 at 500 th. You can change this if you want right from the perturbation/differential view as needed.
Yes, there is an interface that allows you to create you own modifications, or view/edit existing ones. Go to File-> Edit Modifications to launch.
Yes, in the Modifications tool there are examples.
Yes it is. When replicates are selected across samples, the the colors are used to differentiate between samples, so they will be only blue and red (assuming two samples are present). When selecting replicates within a sample, all colors should be different for the spectra and XIC.
Yes the user preferences allow you to create your own series of custom colors. Fonts can also be changed.