Q: Where can i read the publication of this work?
A: Here: http://www.springerlink.com/content/9182882314l6k634/

Q: I have a question that is not in the faq.
A: Email info@omicsinformatics.com anytime!

Q: I would like to try the software on my dataset before committing to purchase. Do you offer a trial version of the software?
A: Yes we offer a free 30 day trial.

Q: How do I zoom in/out in the spectral view?
A: 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.

Q: What is a “peptide set”
A: 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” (this could be csv, pepxml, mascot, sequest, or x!tandem). the required fields for this file are retention time, charge, and sequence. the format for a peptide set is displayed in the protein definition tutorial.

Q: How can I arrange to have PyMol launch automatically?
A: We have a video in our tutorials section. Also feel free to Email info@omicsinformatics.com and we can show you.

Q: My peptide detection does not complete. what could cause this?
A: Make sure you have no empty values in the first four columns of your peptide set. Check that you are running the latest version of 64 bit Java 8 and that MSfilereader is installed. International users may experience detection issues when commas replace decimals. To fix: go to control panel> region and language> format tab > additional settings> next to decimal make use of a (.) instead of the comma symbol.

Q: With which instruments does the software currently function?
A: We currently we support Thermo and Waters high resolution instruments.

Q: Can my ms files contain ms2 data?
A: Yes. The algorithm ignores MS2 data in the undeuterated detect.

Q: I can’t find the peptide by adjusting the retention time bars and the extracted ion chromatogram (XIC).
A: 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.

Q: What are the grey bars surrounding the peaks of my peptide?
A: These are the sub range windows and show where peptide peaks are expected to reside. The software only considers peak data from within these ranges to calculate the centroid. This approach is used to disregard non peak data and also provides a visual reference to confirm your peptide.

Q: How is the width of the sub ranges determined?
A: The width of these ranges is determined by the “mz / ” value in the detect panel. hdx-wb 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 view as needed.

Q: Can I search for modifications?
A: In the t0 detect panel, the “modifications” tab shows all preconfigured modifications. Select one, or multi select several to search for modifications on all peptides. Most of the time the better method will be to look for a modification on a specific peptide. To do this just then, edit the peptide sequence in the peptide set next to your peptide add the modification in square brackets immediately following the peptide sequence. For example the short name for carbamidomethylation on Cysteines is capC. So for the sequence QVTCKRCSY you would enter the peptide sequence as follows: QVTCKRCSY[MOD-capC]

Q: Can I add my own modification?
A: Yes, there is an external xml file called compounds.xml within which this can be accomplished.

Q: Do you support N and C terminal modifications?
A: Yes, in the compounds.xml there are examples of this.

Q: When I select multiple replicates, the overlaid spectra and XIC are sometimes only colored in blue and red, and other times it is colored more than two colors. is this normal?
A: 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.

Q: How is %D calculated?
A: The software can determine the level of deuterium content from both the centroid or from the best scored theoretical distribution. Please read the publications for The Deuterator and HD Desktop for detailed information.

Q: Initial t0 detect did not complete. what could be wrong?
A: Check the peptide set and make sure there are no empty values in any of the fields. if you don have input retention time then put a valid narrow range in each row such as 5.0 – 5.1. if the score field is empty then put in 0. this could also occur if there are corrupt raw files.

Q: I closed the program in the middle of a detect job and now subsequent jobs never finish.  Do i have to set up a new experiment?
A: Rerun the detect and check “rebuild scan files”.