The isoform mass threshold limits the size of isoforms included in the database. You can use the isoform mass threshold to improve search speed by limiting the database entries to only isoforms likely to be found in the sample.

For example, a typical top-down LC/MS experiment is unlikely to detect an intact form of Titin (over 1Mda).

To illustrate the effect of the isoform mass threshold on the number of entries being considered, applying a 70,000 Da threshold to the entire yeast proteome reduces the total number of isoform entries from 6050 to 4550. This 25% reduction speeds up database searching, particularly for subsequence searches.

IMPORTANT

It is important to note that subsequences or truncations of parent sequences larger than the upper mass limit will not be detected. For example, if the upper mass limit is set to 70 kDa, a 25 kDa truncated proteoform from 75 kDa parent sequence will not be detected. In order to detected this truncated species, you must increase the upper mass limit to greater than 75 kDa.

Procedure

  1. Select the gear icon, , in the Database Manager.
  2. The Advanced Parameters dialog box opens.
  3. For Max Isoform Mass, enter a value.
    The default is 70,000 Da.
  4. Select the Save icon.
  5. Continue creating your database. See Create a database from a FASTA format file.