Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Exercise ADM2

Topic

Configure a new nucleic acid database for Mascot Server

Requirements

Administrator access to an in-house Mascot server.

Experimental

Add the h_pylori_pep database to your Mascot Server.

To download the fasta file, right-click this link: h_pylori_26695.seq.fasta, and choose Save target as or Save link as

The first few lines of the database are:

>HP0945.1 tRNA-associated protein (trl) {Helicobacter pylori 26695}
ATGAGTGGTTGTGCGTCTTCTTCGCCAACTGGCACTCTTATCACTATGGTAACGATGCCA
. . .
>HP0001 hypothetical protein {Helicobacter pylori 26695}
ATGGCGACACGAACTCAAGCCAGGGGGGCTGTGGTTGAATTGTTGTATGCGTTTGAGAGC
. . .
TTAAACGCTATCTTGGATTCTTTGAGCAAAAAGCTCACTCAAAAACCCTTGAATTGA
>HP0002 6,7-dimethyl-8-ribityllumazine synthase (ribE) [6.3.3.-] {. . .}

Test the database using the following sequence query with a no enzyme or semi-trypsin search:
813.4 seq(PLANNER)

Tips

  • Suitable parse rules are already defined. You just have to select them

Questions

  • How many sequences are in the database?
  • How many bases are in the database?
  • Do any sequences have any invalid bases?

 

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