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Unassigned peptides list
[Mascot results file module]

Unassigned list in peptide summary reports

In standard Mascot Server peptide summary reports, there is an "unassigned list" at the bottom of the page - for example:

Unassigned queries: (no details means no match)
 Query  Observed Mr(expt) Mr(calc)   Delta  Miss Score  Rank   Peptide
  113   893.28   1784.54   1784.92   -0.37    0    65     1    VGAVAGNDWLIWDITR
  107   882.21   1762.40   1762.79   -0.38    0    62     1    LISWYDNEFGYSNR
  67    691.20   1380.39   1380.64   -0.24    0    61     1    ALEESNYELEGK
  70    695.73   1389.45   1389.67   -0.21    0    60     1    QSLEASLAETEGR

This is a list of MS-MS spectra that have had matches to peptides, but are not included in the main report because the proteins which they are found in have too low a score. If the list of proteins in the main report was not cut off, i.e. if all proteins were displayed, then there would be no unassigned list.

For example, if a query had the following matches, then it would not be in the unassigned list.

RankPretty RankScorePeptideProtein
1178ABCDEFG  
2178ABCDEGFgi|123456
3178BACDEFG  
4465ASDADSD  
5465SDFSGSD  
6612DFGHDFG  
778SSDFDFD  
887RTYRYRY  
994RTYRYRY  
10102TYUTUTU  

Although there was no protein match the rank 1 peptide, the rank 2 peptide had the same score, so this is in effect treated as the top match for the query. The query will then be included under gi|123456.

Unassigned list in protein summary reports

An unassigned list can be created for a protein summary. This list is just the list of peptides that didn't get a match anywhere in the top 50 hits.

Creating the unassigned list

After creating an ms_peptidesummary object, the method createUnassignedList() needs to be called. The parameter is one of:

ms_mascotresults::QUERY

Sort the unassigned list by ascending query number. This is the same as ascending relative mass order.

ms_mascotresults::SCORE

Sort the unassigned list by descending score.

ms_mascotresults::INTENSITY

Sort the unassigned list by descending intensity. Intensity values are taken from the qintensity value in the results file if they are available (pkl files, some MGF files). If these values are not available, then the intensity is calculated from the sum of all the ions values.

Note that for a very large MS-MS file, this option can take some time to process unless there are qintensity values in the results file.

Getting the entries for the unassigned list

Once the unassigned list has been created, use getNumberOfUnassigned() to determine the number of items in the list. You can then retrieve peptide at index i with getUnassigned(i).

See also getUnassignedIsBold() and getUnassignedShowCheckbox().

Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51