Proteoannotator GUI mode
ProteoAnnotator can be run within Proteosuite, which is a tool originally designed for quantitative proteomics, and now incorporating ProteoAnnotator. Here a beta release of Proteosuite containing ProteoAnnotator has been made for demonstration purposes – full release to follow later in 2014. The pipeline can be run in the GUI as follows:
1) Raw MGF data is loaded into Proteosuite, and the genome annotation option is checked. Multiple MGF files may be selected, however these will be merged when the pipeline begins, up to a maximum limit of 1GB or 25000 spectra of merged MGF data: however if the data exceeds these limits, the users will be notified that the pipeline cannot be run.
2) Search parameters and ProteoAnnotator options are set via a form as shown in the image. Many of these options are directly passed on to SearchGUI. Users are expected to enter one official gene set, and optionally add several non-official gene sets, as GFF3 formatted files. GFF3 data for each gene model set is mandatory, however a separate FASTA file containing protein sequences is only mandatory if the GFF3 file lacks protein sequences. Protein sequence data should contain only targets, no decoys - the pipeline takes care of decoy database generation.
3) The pipeline is started using the “Run” button, and the user is later notified when it has completed (future builds will incorporate improved feedback for the user in terms of the length of time to complete the different steps). The output of the pipeline may be inspected in the ‘annotation_output’ folder where the raw data was located. Output items of interest include newly annotated GFF3 file (for each gene model set entered, various mzIdentML files, various CSV files (as described above) and a log file called ProteoAnnotator.txt.
Proteosuite is a tool originally designed for quantitative proteomics, and now incorporating ProteoAnnotator.
Proteosuite can be obtained from: http://www.proteosuite.org/?q=downloads