Tutorial

1.     Workflow: The sidebar has a Work Flow entry which contains the detailed step-by-step description for conducting a di/tripeptide search by PEP Search in MyCompoundID. The user is encouraged to read this description for an overall picture of how PEP Search works. For the user's convenience, this description is also included here as follows (Figure 1).

Figure 1. The workflow of PEP Search.

 

2.     Di/tripeptide Databases: PEP Search in MyCompoundID searches an MS/MS spectrum against a database of di/tripeptides. This database consists of 400 dipeptides and 8000 tripeptides, and their theoretical MS/MS fragments. PEP Search also provides an option to do dimethyl labeling confirmation. This option enables the search against the 8400 di/tripeptide database plus a library, which consists of dimethyl labeled 8400 di/tripeptides and their theoretical MS/MS fragments.

3.     Dimethyl Confirmation: PEP Search provides an option to confirm the identification of di/tripeptides by dimethyl labeling. To do so, the same sample should be dimethyl labeled and analyzed with the same LC gradient on LC-MS/MS. The generated dimethyl labeled spectra should be searched together with the non-labeled LC-MS/MS spectra in a .csv file. The search results provide putative di/tripeptide IDs and the matched dimethyl labeled a₁ ions. If the N-terminal amino acids of the di/tripeptide IDs are confirmed by the dimethyl labeled a₁ ions, their IDs are then confirmed and their match scores are increased correspondingly.

4.     Single Mode Search: Besides batch mode search of LC-MS/MS spectra in .csv files, PEP Search also provides single mode search for manually checking a single MS/MS spectrum by directly input precursor mass, MS/MS fragments and their intensities.

The following demonstrates the flow of using PEP Search in batch mode with input LC-MS/MS data of di/tripeptide standards.

5.     Search Parameters. There are several parameters that need to be set by the user before submitting a query.

Figure 2. PEP Search's interface showing the search parameters.

a.      Mass tolerance. The user can define a search mass error threshold in Daltons (Da).  The default is 0.05 Da, which is applicable for data generated from QTRAP or QTOF mass spectrometer. The ??MH Tol?? defines the mass tolerance of precursor ion, and ??Peak Tol?? defines the mass tolerance of fragment ions in the MS/MS spectrum. The user can specify a mass tolerance threshold based on the mass accuracy obtainable from the user's instrument. Note that adjusting this search parameter will have a significant effect on the number of hits returned for the query spectrum. Please refer to Figure 3.

Figure 3. The mass tolerance thresholds can be entered in Da.

b.      Retention time shift window. For dimethyl labeling confirmation in the search, the retention time (RT) shift window for dimethyl labeled di/tripeptides can be adjusted according to users?? LC gradients in seconds. The RT shift window can help matching non-labeled and dimethyl labeled peptides based on their precursor mass and retention time. From our experience with HILIC separation of di/tripeptide standards,  dimethyl labeled di/tripeptides usually elute earilier than non-labeled peptides. The default RT shift window is set to from -600 sec to +120 sec. Please refer to Figure 4.

Figure 4. The retention time (RT) shift window can be entered in sec.

c.       a1 ion intensity threshold. After dimethyl labeling, the intensity of a₁ ion will be greatly enhanced. To differentiate dimethyl labeled a₁ ions from other fragment peaks, a ion intensity threshold can be adjusted. In default setting, the intensity threshold is set to be 5 times of base intensity, which is the background intensity. Please refer to Figure 5.

Figure 5. The a1 ion intensity threshold can be entered.

6.     Submitting a query. Once all parameters have been set, the user can click on:

7.      Search result display. The result page displays two tables, the parameter table and the search result table. The parameter table is displayed at the top of the page in order to remind the user of the parameters selected for that particular search query. The result table is displayed immediately below. Note that the entries in the result table can be sorted by their retention time.

The result table consists of the following columns:

a.     Number of matched entries. The first column indexes the hits returned for the search query.  

Figure 7. The search result page displaying both the parameter table and the result table. The first column indexes the matched entries for the query.

b.    [M+H]⁺ (mass). The second column shows the monoisotopic molecular mass of the peptide in Da (Figure 8).

Figure 8. The masses in Da of the matched entries are displayed in the second column.

c.     Retention time (min). The third column shows the retention time of the peptide in minute (Figure 9).

Figure 9. The retention time in minute of the matched entries are displayed in the third column.

d.    Unlabeled peptide matches. The forth column displays peptide identifications for the matched entry. The number indicates how many peptide identifications are matched with one entry. By clicking the number in this column, a table containing all identifications for that entry and their scores will be displayed as shown in Figure 10.

Figure 10.  The numbers of peptide IDs for queries shown in the forth column. Each number is linked to an identification table of match scores.

e.     Ambiguous Id: The ambiguous Id shows the first ranked identification entry in the unlabeled peptide matches. By clicking the ambiguous Id, the same identification table as shown in Figure 10 with peptide identification sequence and score will be displayed. Please refer to Figure 11.

Figure 11.  The first ranked ambiguous peptide Id for queries was shown in the fifth column. Each Id is linked to an identification table of match scores.

f.              Dimethyl a₁ ions. The dimethyl labeled a₁ ion matches for one particular precursor mass and retention time window are displayed in the fifth column. Commas separate the possible number of lysine (K) in peptide sequence. If there is no K in the peptide, its matched dimethyl a1 ions are displayed in front of the first comma; if there is one K in the peptide, its matched dimethyl a₁ ions are displayed between the first and the second comma;?? In total, there are at most three K??s in a tripeptide; in this case, the matched a₁ ions in dimethyl confirmation will be shown after the third comma. The dimethyl labeled a₁ ion match also is linked to a table containing peptide identifications and their match scores after dimethyl confirmation. If there is an a₁ ion matched in dimethyl confirmation, the score for that peptide will be increased. Please refer to Figure 12.

Figure 12. The dimethyl a1 ions matched for the query shown in the sixth column. It is linked to an identification table containing peptide identifications and their match scores after dimethyl confirmation.

g.    Confirmed Id: The confirmed Id in the search result table displays the first ranked confirmed peptide identification by matching the ambiguous Id and the dimethyl a₁ ions. By clicking the entries in this column, a table containing peptide identifications and their match scores after dimethyl confirmation. Please refer to Figure 13.

Figure 13. The confirmed Id displays the first ranked identification of peptide after matching the ambiguous Id and the dimethyl a₁ ions. It is linked to an identification table containing peptide identifications and their match scores after dimethyl confirmation.

h.    Matched spectrum. By clicking the peptide identification in identification table, under the column of ??Sequence??, a webpage interpreting the MS/MS spectrum of that identification will pop out. As shown in Figure 14, this webpage contains a MS/MS spectrum (red) match with its theoretical spectrum (blue), and tables listing all MS/MS fragments of that peptide and its hits.

Figure 14. An MS/MS spectrum interpretation webpage for a peptide identification.