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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 6 columns. The first column is the database which you selected before search. The second column is the accession number of the protein in SwissProt database, you can click the accession number to open the protein record in SwissProt. The third column is protein name. The fourth and fifth column is the molecular weight and the isoelectric pointof the protein. The sixth column 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.And the seventh column is the iTRAQ value of the protein in each sample. You can click "Show ratio" to open the corresponding detail information page of protein content in each sample ( including the parallel analysis ).
Figure 2. browse the protein level data
As shown in Figure 3, The peptide level data of the protein include 17 columns. The first three 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 fifth column) of them as represent. you can display all these peptide level records by click the peptide sequence in the fourth column. The other columns are the iTRAQ information of the corresponding peptides in each sample.
Figure 3. the peptide level data
After you click the peptide sequence "gEPPLPEEDLSk" of Figure 3, the detail peptide level data will be show as in Figure 4. The columns include the detail information of peptide, including the observed m/z, the actual peptide mass, the actual minus calculated peptide mass and total ion current of the highest ion score peptide and the iTRAQ informationas 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 search" and input the protein accession of SwissProt in the text box, or you can select "peptide search" and input the sequence of the peptide 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. Click "show peptide" will open the peptide level data of the selected protein line. And click ˇ°show ratioˇ± will open the iTRAQ quantification information 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. Third, the quantification infornmation of the peptides in each run was given in peptide level results.
Figure 7. Peptide level data
Figure 8. peptide detail information page