Query COPaKB with an mzML File

You can analyze proteins in a mass spectrum file using Query COPaKB(mzML File) utility of the COPaKB. Your input data can be in the mzML or Raw (Thermo Scientific) format. If your file is in Raw format, you can optionally convert it into mzML using the ProteoWizard Converter before using COPaKB for data analysis. (Note: if you would like to conduct a batch analysis of multiple data files, please use COPaKB Client program).

Query COPaKB (mzML File) has two sections: "Spectral Analysis" and "Search Report". To start an analysis, you can use the "Spectral Analysis" section. To retrieve a completed data analysis, you can use the "Search Report."


To start an analysis, enter your email address and select a COPaKB module of your sample.


Then, you can load your data file in the "Local Data File" section.


Alternatively, you can choose a file from the web (http or ftp) as input.


You can also specify the parameters of your mass spectral analysis by unchecking the checkmark in front of "Use Default Parameters"


When you click the "Upload & Search" button, your spectral data file begins to upload.

A task ID (e.g., 14323) is created when uploading is completed. Now, you can review the progress of your analysis by clicking on this ID, even when the analysis is still ongoing.


This leads you to the summary of your analysis (see the picture below). The latest updates on the analysis are appended to existing report when you refresh this page.


Moreover, you can review a specific peptide by clicking on the sequence. You can also review a specific mass spectrum by clicking on its spectrum icon (see the picture below).


After your analysis is completed, a report is generated. It provides an index of all proteins and spectral matches identified in your data file (left pane). Relative abundances of these proteins are assessed by values of Normalized Spectral Abundance Factor (right pane). The results can be saved in Excel-compatible format or COPaKB Client-compatible format.


By clicking on a protein in the left pane, you can review their sequence and imaging profiles in the right pane. (Note: if you experience technical difficulties reaching the following two pages with IE 9 or IE 10. Please use IE 8, Firefox, Chrome or Safari.)


By clicking on a mass spectrum icon in the left pane, you can also review the spectral match in the right pane.


You can also view the role of a selected protein in heart diseases and the existing data on the protein's transcriptional control mechanisms in the right pane.


The results of a previous analysis can be retrieved for you to review when you enter the correct combination of its task ID and email address.