This dialog allows for the altering of the advanced SearchGUI settings.
Most search engines are able to take advantage of so-called multithreading. Meaning that more than one process can be carried out at the same time. As a default SearchGUI allows the search engines to use as many threads as there are processors on the running machine. Using more is not possible, but the number can be reduced, for example if the machine is to be used for other tasks at the same time.
Before using a spectrum file SearchGUI validates the file. This includes checking if the file
has been peak picked and if there are duplicate spectrum titles. Both options can be switched
off in this dialog. This is however not recommended unless there are special circumstances.
The size of the spectrum files is also checked, as very big spectrum files can cause issues
for some of the search engines. For example OMSSA does not seem to be fond of mgf files bigger
than around 1 GB. In such cases it is therefore recommended to split the mgf file into smaller
parts than can later be merged when processing the search results in PeptideShaker. In this
dialog the maximum mgf file size before SearchGUI suggests that a spectrum file should be split
and how many spectra to include in each new spectrum file can be set.
When SearchGUI adds reverse decoys to a given FASTA file it generates a new file with the
same name as the original FASTA file plus a suffix at the end.
SearchGUI also renames the search result file generated by X!Tandem. This option can here
be switched on or off.
Running SearchGUI can often result in a long list of output files for each search engine, especially when searching multiple spectrum files. To better organize the files SearchGUI supports various types of output file formatting: (i) Single zip file - Groups all files in a single compressed zip folder, (ii) One zip file per mgf - Groups files per run (i.e. spectrum file), (iii) One zip file per algorithm - Groups files per identification algorithm, and (iv) No zipping - No file grouping. In addition one can choose if the spectrum and FASTA files are to be included in the zipped files.
If the data is to be processed in PeptideShaker a peptide to protein mapping, referred to as a protein index, has to be created. The protein index is only created the first time a given FASTA database file is used. It is recommended to create the protein index parallel to running the search engines. This option can be turned off by setting this option to 'No'. The index will then instead be created when loading the data in PeptideShaker.