Figure 1

Summary of ATAQS workflow. ATAQS is composed of seven steps. The data flow is flexible in that the user can select which steps they want to use in cases in which the whole pipeline is not used. For example, if the user has already generated and optimized the list of transitions and decoy transitions, then the user can skip steps 4 and 5. In each step, there are major options for user to select or define. In step 1, the experiment needs to be annotated by selecting exact mass spectrum instrument and organism. Also, the user can select other researchers who can share the project. In step 2, the user needs to provide or select a list of proteins. In step 3, the user can explore the selected proteins' properties and interactions by using PIPE2. Then, the user can extend the protein list or trim it down to a smaller number of proteins. In step 4, the user needs to define what type of peptides and transitions to be selected for a given protein by specifying penalties of amino acid compositions and fragment ion types. In step 5, the user will select to generate a decoy or heavy/light pairs based on user-selected decoy generating algorithms and labeling methods. In step 6, mzXML or mzML format of measured data set is selected and the user groups the experiments by transition list. Then, user can also select transition property measuring algorithm in this step. Based on the results of step 6, the user can choose a FDR cutoff to determine validated peptides in a given sample. In step 7, as an option, the user can create a TraML format of verified transitions to share with the community.