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Hunt Lab Software Tools

Donald Hunt

 

Download the CAD Neutral Loss Finder

 

Program Description: Searches CAD spectra for user-defined neutral losses by calculating the average mass of the expected peak corresponding to the loss (given the charge state of the precursor mass). Thus, it assumes data acquired with high resolution precursor masses and low resolution fragment masses. It filters the potential candidate spectra using an intensity threshold and a requirement that the loss peak be one of the more abundant peaks in the spectrum (both user-defined parameters). It creates two output files in comma separated (.csv) format. The first is a list of all CAD spectra containing potential neutral losses. The second contains a more concise list that merges results for the same precursor mass as it elutes over time. These can easily be imported into Excel for further analysis.

 

CAD Neutral Loss Finder is written in Java and requires installation of the Java Runtime Environment.

 

Input files must be .mzXML format. We have tested only data acquired on Thermo instruments, using ReAdW.exe for conversion to .mzXML. ReAdW.exe is a product of the Seattle Proteome Center at the Institute for Systems Biology. It requires the XRawFile library from Thermo and must be run in Windows.

 

The program also requires the open source jrap libraries available from the Institute for Systems Biology. You can place the libraries in a 'lib' folder in the same directory where CAD Neutral Loss Finder resides.

 

We hope you find the software helpful. If you use our software for work that results in publication or presentation, please reference this web page.

 

Funding provided by National Institutes of Health grants to D.F.H. (GM037537 and AI033993).