SPS docs - analysis

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| {color:#000080}{*}P{*}{color}{color:#000080}{*}ar{*}{color}{color:#000080}{*}ameter name{*}{color} | {color:#000080}{*}Valid values{*}{color} | {color:#000080}{*}Default{*}{color} \\ | {color:#000080}{*}Description{*}{color} |
| RELATIVE_DIR \\ | 0/1 | 1 | Specifies if paths should be treated as relative. If set to 0, the project directory absolute path is calculated and prepended to all relative paths to files used and generated internally. This is useful in environments where absolute paths are needed. \\ |
| PEPNOVO_PTMS | string | empty \\
string | Specifies known PTMs that should be considered when generating scored PRM spectra from MS/MS spectra. C+57 and M+16 are always considered even if this parameter is not specified. PTMs do not need to be specified here to be reported in resulting analysis since SPS is fully configured to handle unknown PTMs for both de novo sequencing and database matching of de novo sequences. CAUTION: Specifying multiple PTMs beyond the most abundant can significantly degrade the quality of PRM spectra (and resulting analysis) - it is not recommended to specify more than six. \\
Each PTM identifier must be separated by a ":" - See here for [here|https://bix-lab.ucsd.edu/display/CCMStools/Setting+PEPNOVO_PTMS] for a list of all current PTM identifiers and how to specify new ones. |
| TOLERANCE_PEAK | 0.0 - 0.4 | 0.4 \\ | Peak mass tolerance (in Daltons). |
| TOLERANCE_PM | 0.0 - 3.0 | 1.5 \\ | Parent mass tolerance (in Daltons). \\ |