1. Browse the database.
As shown in Figure 1, First, select the "Browse" tab of the Website menu bar. Second, select the database which you want to search, then click the "Browse" button, the protein level date of the database will be show.
Figure 1. browse the database
As shown in Figure 2, The browse result of protein level including 11 columns. The first column is the database which you selected before search. The second column is the accession number of the protein in SwissProtdatabase, you can click the accession number to open the protein record in SwissProt. The third column is protein name. The fourth column is the exclusive unique peptide count of the protein. The fifth column is the total spectrum count of the protein. The sixth column is the percentage sequence coverage of the protein.The seventh and the eighthcolumns are the molecular weight and pi value of the protein. The ninth column is the signal intensity of protein. The tenth column is the iBAQ value of the protein. The last column of the browse result tables is the peptide level information of the protein, you can click "Show peptide" to open the corresponding detail information page of peptide level data of the protein.
Figure 2. browse the protein level data
As shown in Figure 3, The peptide level data of the protein include 16 columns. The first six columns of the table is same as the protein level data. Because same peptide sequence may include multiple records, we merged these peptide record and show the data with the highest ion score (the eighth column) of them as represent. you can display all these peptide level records by click the peptide sequence in the seventh column. Note that, same peptide sequence with different fixed modification (the tenth column) or variable modification (the eleventh column) will not be merged as same record. The other columns are the number of enzymatic termini, the observed m/z, the actual peptide mass, the actual minus calculated peptide mass and total ion current of the highest ion score peptide. The spectrum charge include all different charges of data set which be merged.
Figure 3. the peptide level data
After you click the peptide sequence "AAANAVLQDK" of Figure 3, the detail peptide level data will be show as in Figure 4. The columns of the table is same as the peptide level data in Figure 3.
Figure 4. 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 SwissProt protein accession) or peptide sequence (middle sequence of the peptide). As shown in section 1 of Figure 2, if you want to search by protein, you should select "protein" and input the protein accession of SwissProt in the text box, or you can select "peptide" and input the middle sequence of the peptide which not include the previous amino acid and the next amino acid in the text box. Second, you should select the display mode of the search result, which include protein level or peptide level as described before. Third, you should select the database which you want to search. At last, click "Query" button, the result will be show.
Figure 5. search the database
3. Use protein level data.
The search result of spectrum data can be shown in protein level or peptide level. Protein level data is shown in Figure 6, there are some function section to use the result data. In section 1, you can input the keywords of any column data to quadratic search the result data. In section 2, you can click each column of the title line of the result table , which will sort the result records according to the column you clicked. Click the "Accession" column will linked to SwissProt database. And click "show peptide" will open the peptide level data of the selected protein line.
Figure 6. protein level data
4. Use peptide level data.
The search result of peptide level data is shown in Figure 7, First, you can quadratic search the result data or sort the result data by click one column of the title line same as in protein level data. Second, the same peptide sequence with the same modifications (fixed and variable) has been merged to the highest ion score record of them to represent. You can click the peptide sequence to open the detail information of each peptide record, as show in Figure 8. The function of quadratic search and sort the result data by each column also can be used in peptide detail information page.
Figure 7. peptide level data
Figure 8. peptide detail information page
5. Biomarker information
As shown in Figure 9, the biomarker application information including 11 columns. The first and second column is the gene symbol and gene name. The third and forth column is the location and the family of protein. The fifth column is the acession number in SwissProt database. The last column is the biomarker applicaton details for each protein.
Figure 9. Biomarker applications of protein