The spectral networks analysis of a dataset starts by executing specnets('myparameters.params'); from the Matlab command prompt. All parameter values, including the name of the file containing the MS/MS spectra, are specified in the parameters file myparameters.params. Of course, you can choose any file name for the parameters file and multiple parameters files can coexist in the same directory.
The parameters file is a text file where comment lines start with '#', empty lines are ignored and parameters are specified using the format PARAMETER_NAME=PARAMETER_VALUE. The valid parameter names and ranges of values are given below.
| Parameter name | Valid values | Description |
|---|---|---|
| INPUT_SPECS | Any valid filename | Name of the file containing the MS/MS spectra. Valid file formats are MGF, mzXML, ms2 and multi-spectra pkl. Note that a database of protein sequences is not required if you only want to find networks of related spectra. |
| EXE_DIR | Any valid path | The directory where you installed and compiled the Spectral Networks package. |
| Parameter name | Valid values | Description |
|---|---|---|
| FASTA_DATABASE | Any valid filename | Database of protein sequences in FASTA format. |
| MIN_SPECTRUM_QUALITY | 0.0 - 1.0 | MS/MS spectra with inferior quality scores are discarded. Default value is 0.15. |
| TOLERANCE_PEAK | 0.0 - 1.0 | Peak mass tolerance (in Daltons). Default value is 0.5. |
| TOLERANCE_PM | 0.0 - 3.0 | Parent mass tolerance (in Daltons). Default value is 1.0. |
| MAX_MOD_MASS | Any number >0 | Maximum mass for a post-translational modification (in Daltons). Use absolute values for negative mass offsets (e.g. loss of water). Default value is 100. |
| MIN_RATIO | 0.0 - 1.0 | Minimum percentage of matched intensity in a spectral alignment. Default value is 0.4. |
| MIN_PVALUE | 0.0 - 1.0 | Minimum p-value to accept an alignment. Default value is 0.05. |
| MIN_MATCHED_PEAKS | Any integer >0 | Minimum number of matched peaks in a spectral alignment. Default value is 4. |
| TAG_LEN | Any integer >0 | Length of the sequence tags used for pattern matching identification of peptides. Default value is 6. |