1. Browse the database.
    As shown in Figure 1, first, click on the "Browse" tab at the toolbar; select the database which you want to search; then click the "Browse" button, and the protein level result of the database will be displayed. (Figure 2)
                Figure 1.  browse the database

    The protein level result includes 10 columns (Figure 2). The first column shows the database which you selected. The second column shows the Swiss-Prot accession number of each protein, which also provides the hyperlink that enable you to browse the protein information in the Swiss-Prot database. The third column shows the protein name in the Swiss-Prot database. The fourth column shows the unique peptide count. The fifth column shows the total spectrum count. The sixth column shows the sequence coverage percentage.The seventh column shows the molecular weight of the protein. The eighth column shows the iBAQ value of the protein. The ninth column show the estimated concentration of the protein. The last column shows the hyperlink to the peptide information of the protein, In addition, you can filter the resulting dataset by input in any data inside the table to the search textbox, and sorting the dataset by clicking each column head.
                Figure 2.  browse the protein level data

    When you browse "normal" database alone, two additional columns will be shown as in Figure 3. They display the quantitative information of the protein, including the relative intensity by the iBAQ method, and the estimated protein abundance (g/L).
                Figure 3.  browse the "normal" database alone

    As shown in Figure 4, the peptide level result of a protein includes 16 columns. The first six columns show the same content as that in the protein level result of the counterpart protein. The following columns show the identification information of the peptide. If a unique peptide has multiple spectrum identifications, we actually display the information of the peptide's spectrum with the highest Mascot ion score, except "fixed modification"(the 10th column),"Variable modification" (the 11th column) and "Spectrum charge"(the 14th column). The column of spectrum charge displays all the spectra charges of the peptide. You can also filter or sort the resulting dataset as described above in protein level result.
                Figure 4.  the peptide level data

     When you click the peptide sequence "VGWEQLLTTIAR" in Figure 4, the spectrum identification information of the peptide will be shown as in Figure 5, which has the same columns as the peptide level data in Figure 4.
                Figure 5.  the detail data of peptide level

2. Search the database by protein accession or peptide sequence.
     You can search the database by protein accession (only support the Swiss-Prot protein accession) or peptide sequence (Figure 6). First you select "protein" and input the Swiss-Prot protein accession in the text box, or select "peptide" and input the middle sequence of the peptide (not include in the first amino acid and the last amino acid). Second, you select the display level of the search result, which includes protein level or peptide level as described before. Third, you select the database which you search. Then click "Query" button, and the result will be shown.
                Figure 6.  search the database

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