Exercise DIS2
Topic
Submit a search of LC-MS/MS data from Distiller and use de novo on a spectrum that failed to get a match
Requirements
User access to any Mascot server, including the Matrix Science public web site
Download Mascot Distiller and install it. To get a free 30-day licence, send an email request to support@matrixscience.com.
Experimental
The Masslynx raw file qtof10348.raw and the Distiller project file qtof10348.rov need to be in the same directory. Open the project file in Distiller.
Submit a Mascot search of all the peak lists and browse the results in Distiller. Use SwissProt, Trypsin, 2 missed cleavages, 0.5 Da / 0.5 Da, no modifications, and the ESI-QUAD-TOF instrument
Data
Right-click this link: qtof10348.exe, and choose Save target as or Save link as. The downloaded file is a self-extracting archive, double-click to unpack the data file (which is really a folder called qtof10348.raw)
Right-click this link: qtof10348.rov, and choose Save target as or Save link as.
Tips
- To save time, you are starting from a project file where peak picking has been completed. You do not need to create a new Distiller project from the raw file (unless you wish to do so).
- At the end of this exercise, save the project for use with exercise SQ3
Questions
- Try to find a peptide match for the summed spectrum of scans 1616-1624 using denovo
- How can you decide whether to accept the de novo solution?