| Back to Data Analysis section |
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Here you can download the database(s) that you will have to use in your searches for the experiment.
The original database is composed by all proteins from ECOLI extracted from the Swiss-Prot database, and also contains the sequences from the four spiked proteins (see Sample description page). In total = 4363 + 4 proteins.
In order to retrieve a False Discovery Rate (FDR) in your searches, we provide, in addition to the normal database (FORWARD database), a RANDOM database and a DECOY database.
The RANDOM database has been created using a ProteinScape scrip that generate a database randomizing the amino acids for each protein sequence in the FORWARD database.
The DECOY database has been created concatenating de FORWARD database and the DECOY database and is the one that we recommend to use as possible. |
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Important: MASCOT provides an option for automatic decoy search. With this option, it is not necessary to create and install a decoy or random database in order to obtain a False Discovery Rate (FDR) estimation. However, in order to minimize the variability between different decoy searching approaches, we recommend installing the DECOY database (FORWARD + RANDOM) in your MASCOT server and then calculate manually the FDR. |
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In case of the ProteoRed Phenyx server, we have installed the DECOY database and we have called it: PME5_ForwardDecoy (indicating that is composed by the FORWARD and the RANDOM database). |
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| Instructions for installing databases in your local MASCOT server |
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- As we have stated previously, we recommend installing the DECOY database (FORWARD + RANDOM) in your MASCOT server and then calculate manually the FDR.
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- Rule to parse accession string from all three databases: ">..|\([^|]*\)"
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- Rule to parse description string from all three databases: ">[^ ]* \(.*\)"
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- An exhaustive description about how to install these databases in MASCOT has been written here:
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How to install the PME5 sequence databases in MASCOT |
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| Instructions for generating the FDR pept matches report in PHENYX |
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As you can see in the GeneBio's wiki page here, Phenyx provides a way to calculate the FDR from your results. |
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Steps: |
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- Search your peak-list using the database called PME5_ForwardDecoy
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- In the main page of phenyx, select your job ID and click on "Exports" option at the left of the screen.
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- Select the "false discovery rate pept matches (excel)" option.
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- In "extra
arguments" wrrte: --acregexpfalse='rnd.+' in order to indicate that the search has been run on a concatenated version of a forward and decoy databank, and that all AC from the decoy databank start by "rnd".
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| Back to Data Analysis section |
