question regarding ATAQS use

[William Slade]

Hello and congratulations on such an  impressive piece of software. 

Currently, i'm attempting to use ATAQS to assist in the development of MRM for mouse proteins. My goal is to assess the ATAQS workflow before dedicating more computer and server space, so i'm using the virtual image via Virtual Box for the time being. I'll state what i'm doing, what is going wrong, and perhaps we can work through how to fix it. 

First, it is necessary for me to discard the saved state of the Virtual image to obtain mouse and keyboard function. After booting centos, I manually start tomcat and mysqld (as root). After logging into ATAQS, i'm able to create new projects and upload protein lists. I then send this list to PIPE2, and, as stated in the ATAQS user guide v1.0 (http://tools.proteomecenter.org/ATAQS/ATAQS_UserGuide-Tutorial.pdf) I send that list back to ATAQS. Although the proteins are now listed under the "validate" tab, I am not prompted with a "save" option, nor is there a button to do so. Thus, i'm stuck with the "generate" tab green, and the "validate" tab yellow. If I try to generate a transition list anyway (either using peptide atlas or uploading my own list) I receive an error when I click "download" transitions. Is this a common error? Shall I attach a screenshot?

Thanks so much for the consideration! I look forward to trying out ATAQS in our workflow.

Best,

Will