Overview: Let's face it, looking at SEQUEST output is complex. That's why we've created this interactive tutorial. Below is an image map of a typical SEQUEST browser summary page. Move your mouse over regions of the summary page to view information about controls or SEQUEST parameters. If you move your mouse over hot spots (you'll see your cursor change from a pointer to a hand) you can read more information about the controls or parameters by clicking on the hot spot. For most efficient viewing and clicking, set your monitor resolution to at least 1024 x 768 and blow up your browser to full screen. Viewing is best with Internet Explorer. Enjoy!
The MS/MS spectrum number. Clicking on will sort the list by MS/MS spectrum number. Back to top.
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TIC
The total ion current of either the MS/MS scan, zoom scan, or full MS scan depending on the state of the Intensity radio buttons. Clicking on the button will sort the list by TIC from highest to lowest. Back to top.
> 5 E+5
File
The scan number(s) of the MS/MS spectrum that was submitted for SEQUEST analysis. Clicking on any individual scan number will show the OUT file (SEQUEST search results) for that particular MS/MS spectrum. Clicking on the button sorts the list of searches by scan number. Back to top.
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z
The charge state of the candidate peptide. The charge state is determined experimentally from a zoom scan if it is available. Clicking on sorts the list of searches by charge state from lowest to highest. Back to top.
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dM
The delta mass between the experimental mass and the candidate sequence identified by the SEQUEST search. dM is computed as Mass(candidate) - Mass(experimental). Clicking on the button will sort the list by dM from lowest to highest. Back to top.
< 1
MH+
The experimental mass of the peptide (M+H) determined from the full scan LC/MS spectrum. Clicking on sorts the list by M+H from lowest to highest. Back to top.
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Xcorr
The cross correlation value computed from cross correlation of the experimental MS/MS spectrum vs. the candidate peptides in the database. The candidate peptide producing the highest Xcorr value is chosen as the #1 hit by SEQUEST. Clicking on will sort the list by Xcorr value from highest to lowest. Back to top.
> 2.0
dCn
The delta correlation value between the #1 hit and the #2 hit in the search. Cn is the normalized correlation (normalized to 1.0). dCn is the delta Cn between the top 2 hits in the search. This is an indcation of the similarity of scoring of the top hits. Clicking on will sort the list in order of decreasing dCn. Back to top.
> 0.1
Sp
The preliminary score obtained during the database search. The Sp is the initial scoring parameter that is calculated based on the # of ions from the MS/MS spectrum that matched the candidate peptide. The initial 500 peptides ranked in the preliminary scoring are submitted for final correlation analysis. Clicking on sorts the list from highest to lowest Sp values. Back to top.
> 500
RSp
The ranking of the peptide after the preliminary scoring. Clicking on sorts the list from highest to lowest RSp. Back to top.
< 10
Ions
The number of matched ions in the experimental MS/MS spectrum versus the total number of possible sequence ions for the identified candidate peptide. Clicking on the ions link (e.g., 17/20) will show the MS/MS spectrum labeled with theoretical sequence ions from the candidate peptide. Clicking on will sort the list by ions matched. Back to top.
> 60% match
Ref
The database reference i.d. number from the protein found in the database search. Clicking on will sort the results by reference in alphabetical order. Back to top.
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+n
The number of times that the candidate sequence appears in the protein database. Multiple entries of the same sequence in the database are due to homology. Back to top.
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( )
The amino acid in the protein preceding the first amino acid in the sequence found in the database search . For example, if a tryptic digest was performed you will generally see a (K) or (R) preceding the sequence. Clicking on will sort the results by preceding amino acid. Back to top.
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Sequence
The amino acid sequences displayed are the #1 hits obtained from each of the individual SEQUEST database searches. Clicking on a peptide sequence will submit the sequence for a blast search. Clicking on the will sort the amino acid sequences in alphabetical order. Back to top.
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SEQUEST Browser Controls
Description of What the Control Does
Shows the Consensus view, which groups together all of the search results (hits) containing peptides from a common protein. The consensus view is shown in this example. Back to top.
Display a "stick" chromatogram which has labeled the location of MS/MS scans and the corresponding proteins identified. Back to top.
The Show/Hide button is a toggle. Clicking Show provides additional controls for selecting OUT files for deleting or copying to another SEQUEST directory. The additional controls include select All, None, Invert, and Execute as described below. Toggling the Hide button will return the browser to the default state with the extra controls hidden. Back to top.
Select All, None, or Invert the state of OUT file selection. These buttons are not visible in the browser until the Show controls button is toggled. Back to top.
The Execute button is used to execute a copy or delete of selected OUT files. The action of the Execute button is dependent on the state of the drop down box shown below. Back to top.
Perform various operations on the currently selected DTA and/or OUT files when the Execute button is pressed. All actions require that you enter your initials in the operator field. Options are described below:
Clone, No OUTS: Copy the selected (box-checked) DTAs to a new directory without the including the OUT (SEQUEST results) files. This operation requires you to provide a new directory tag.
Clone, With OUTS: Copy the selected (box-checked) DTA and OUT files to a new directory. This operation requires you to provide a new directory tag.
Delete Both: Delete both the selected DTA and OUT files from the current SEQUEST directory.
Delete OUTs: Delete only the selected OUT files keeping the DTA files in the current SEQUEST directory.
Clone Tsunami!: Copy the selected DTA files to a new directory and perform a new SEQUEST search using the original database which has the contaminants.fasta database appended to it. In order to perform this step you must first use the database indexer which is available from on the SEQUEST utilities (local MS utilities) page. The clone operation requires you to provide a new directory tag.
Make Tsunami database: Create a combined database containing the contaminants database and the database(s) used for the currently displayed search results. Index the databases as described above before using this feature.
Copy to...Copy the selected DTA and OUT files to one of the available reference directories. The reference directories are used to exclude common contaminants from being searched with the IonQuest feature.
The operator's initials. The user must enter his/her initials here in order to Execute any of the directory-based operations. Back to top
Enter Tag for New Dir:
mydirectory_
If a new directory is cloned, the SEQUEST browser requires that you provide a new tag which is appended to the current directory name. The system will not allow you to overwrite the current directory during the cloning step. Back to top
The checkboxes are used to select OUT files individually, for copying or deleting with the Execute button. Back to top.
Activate the DTA VCR which allows you to conveniently flip through the MS/MS spectra of each search result. Back to top.
Intensity: Full Zoom MS2
Select the intensity displayed in the TIC column, either from the Full MS scan, Zoom scan or MS/MS scan. Back to top.
Max rank:
This parameter should be called minimum rank, because in order for any particular hit to be grouped as part of a consensus, it must have attained a minimum ranking in the SEQUEST scoring as indicated in the input box. For example, with a value of 3, any of the top 3 hits in a search could be included in a consensus grouping. This is useful as the correct hit is not always the #1 hit in the score list, often because of sequence homology or other factors (e.g., poor spectral quality). Back to top.
Max list:
The maximum number of proteins in the final consensus grouping, which is shown at the very bottom of the summary page. Back to top.
Dir:
The name of the current SEQUEST directory where all OUT files and DTA files are stored. Clicking the directory link allows you to view the directory contents. Back to top.
Db:
The name of the database used in the SEQUEST search, and the date the database was created. Back to top.
Navigation bar
Click on the links in the Nav bar to access other parts of the SEQUEST browser. Back to top.
Inspector
View information about the status of the SEQUEST searches, showing the DTA files which were searched and the length of time required to perform each search. Back to top.
View Info
View a log file which shows all operations performed on the current SEQUEST directory. Back to top.
will sort the list by MS/MS spectrum number. 
button will sort the list by TIC from highest to lowest. 
button sorts the list of searches by scan number. 
sorts the list of searches by charge state from lowest to highest. 
button will sort the list by dM from lowest to highest. 
sorts the list by M+H from lowest to highest. 
will sort the list by Xcorr value from highest to lowest. 
will sort the list in order of decreasing dCn. 
sorts the list from highest to lowest Sp values. 
sorts the list from highest to lowest RSp. 
will sort the list by ions matched. 
will sort the results by reference in alphabetical order. 
will sort the results by preceding amino acid. 
will sort the amino acid sequences in alphabetical order. 
