Thursday, February 13, 2014

Create complex projects with ease in PEAKS 7

One of the issues in previous version of PEAKS is the difficulty on creating large, multiple sample projects. Users have to make hundreds of mouse clicks to create a project with hundreds of samples.

Introduced in PEAKS 7, the new project wizard has all the functionality in the previous versions and provides additional controls to make creating complex project easily. You can still use the new project wizard the exact same way as it is in the previous version to quickly create simple projects containing only a few fractions and samples.

Below is a screenshot of the new project wizard interface. The portion in the red rectangle is the new controls introduced in PEAKS 7. It essentially provides a staging area for all related data files, a search function to help quickly highlighting multiple files and control buttons to add the highlighted files to the project in different ways.

You can use the "Add Data" button to add data files to the staging area. The files will be listed in the white box on the left. Once the files are listed there, you can then type a few characters in the search box to highlight files of interest. PEAKS will gray out the files that do not match the search and pull all the matched files to the beginning of the list.

Once you have one or multiple files selected in the staging area, you can use one of the three buttons to add them into the project.
The first button will create a new sample and put all the selected files under the new sample as fractions. This is equivalent to adding multiple files to one sample in the old way. The second button  will create a new sample for each selected files. This is very useful when creating a PEAKS project with hundreds of samples. The third button is to be used to add more fractions into an existing sample. The forth button is to be used to remove samples and/or fractions from the project.

The new project wizard also integrated the most commonly used analytical workflow in PEAKS, starting from data refinement (data pre-processing) to peptide/protein identification, including PTM analysis and mutations. The workflow may include label free quantification if the context is applicable.



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