DEX – Extra-Programs

Extra Programs       

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Width programs

 

Some users have found it relevant to determine the range or width of the mass spectrum envelope that is within a certain percentage of the highest part of the envelope.  For example, what is the range for a whole protein mass envelope that has at least 50% of the maximum signal?  This range would be the central portion of the profile, where the signal is highest. 

 

Original Spectrum (including entire protein spectra) widths

To determine what the range that satisfies a specific percent of the highest part of the signal you this format:

 

original-spectrum-width  lower  upper  filename  percent-width

 

Where “lower” is the lowest part of the spectrum you want to consider, “upper” is the upper end of the envelope you want to consider, “filename” is the name and location of the undeuterated raw mass spectrum file and “percent-width” is the user-defined width for determining the range.  “percent-width” should be an integer between 1 and 99.  Besides the user-defined value, the program automatically calculates the width, upper and lower values of the range and number of points for a 20% width and a 50% width. 

Note:  This program will actually work better on lower resolution data, where the entire envelope is rather smooth and bell-curve shaped.  For spectra where the peaks of the populations are clearly evident and the signal between the peaks falls noticeably, the resolution should be high enough to deconvolute the data first and then use the second program to determine the width of the profile.  Click here to go to the DEX-Install-Tutorial to use DEX to deconvolute peptide spectra.

 

Deconvoluted peptide profile widths

To determine the peaks that fall within the user-defined limits for peptides that have been previously deconvoluted with DEX

use the following format:

 

HD-populations-width  filename  both  start_offset  data_type  align  percent-width

 

Where “filename” is the name and location of the deconvoluted file you want to determine the widths for, “both” specifies that you want to print out all the information, start_offset is almost always the value “1.5”, data_type is either “1” to determine the width of the profile for the deconvoluted backbone amide populations and “2” is to determine the width of the profile for the undeconvoluted mass spectrum profile.  “align” tells the program to automatically align the peaks for you and lastly the “percent-width” is the user-defined width to determine the range.  The percent-width should be an integer from 1 to 99. 

To run this program using the example data provided in this package, type:

 

 

This will find the populations for all the peptides in the file time-10min.dat as well as the peak range for each.  The results of this program will be the same as the results of the HD-populations program with the addition of some information on the profile width after the centroid of each peptide is listed.  The information includes the starting and finishing peak that satisfy each percent, the width between the peak range and number of bumps.  The second set of information includes the linear interpolation of the integrated peaks to create a smooth profile.  This is a more exact method of determining the peak width, as it is more sensitive to peak heights.  The bumps will be zero if the population envelope is smooth, and if the bumps is greater then zero then you may have different types of deuteration events occurring.  The two standard profile widths are 20% and 50%, while the user-defined one is listed immediately after these two.  First the range, width and number of bumps is listed for the “%Weights” column, which attempts to determine the profile’s relevant peaks.  Like the HD-populations program, sometimes the %Weights column is not long enough, and so the “Percent” column is also displayed underneath the %Weights column.  Generally, the ends of the envelope is not too important for the peak widths, but the values may be misleading if you have an extra contamination peak you wish to avoid.  Simply use only the values you want and recalculate the peak width manually in this case.  If you want to save this file and not display the results to the screen type:

 

 

Where the “>” will redirect the output to the file “examples/time-10min-width.dat”.  You can then view the file by typing “vi examples/

time-10min-width.dat” and view the saved output. 

 

Update

Written by Matthew Hotchko and last updated last on March 2, 2006

 

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