New Project
Introduction
The New Project dialog is where new PeptideShaker projects are created based on identification files.
After completing each field click "Load Data!" to start the processing. During the importing of the files
the progress of the import will be displayed.
To open previously saved projects use the Open Project option instead.
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Project Details
The project details will be used to reference the project. It is possible to set the project name, the type of sample and
the number of the replicates. The project annotation is mainly there to help you annotate the project with the information
you find important for later re-use of the project.
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Input Files
PeptideShaker requires information found in three different types of files:
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Identification File(s): the files containing the identification results. Supported formats are OMSSA OMX files, X!Tandem XML files and Mascot DAT files.
If the identification files were generated using SearchGUI, PeptideShaker will
load the additional files automatically!
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Spectrum File(s): the files containing the peak lists used for the search in the
MGF format.
All spectra should be provided and uniquely entitled! To generate compatible MGF files we recommend the use of ProteoWizard.
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Database File (FASTA): the FASTA file used to identify the spectra.
Identification should be conducted using concatenated Target/Decoy databases. The tag for reverse sequences is "REVERSED".
We recommended using SearchGUI for the identification of spectra.
Peptides common to the Target and the Decoy database will be automatically ignored. See also Database Help.
Loading big files can require a lot of time and memory. We recommend trying PeptideShaker on smaller datasets first!
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Processing Parameters
Additional settings can be set for the preprocessing of the identification files:
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Search Settings: The search parameters should be set carefully in order to process the data reliably.
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Import Filters: Filters on the search engine e-values, the peptide length or the precusor accuracy can be added.
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Preferences: Various processing parameters can also be fine tuned.
If the identification files were generated using SearchGUI,
PeptideShaker will load the search parameters automatically!
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