SPS docs - analysis

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| TOLERANCE_PM_PPM \\ | any number > 0 | none if not specified | Parent mass ppm tolerance. This is only used for clustering with PrmClust. |
| RANK_FILTER | any integer >0 \\ | \-1 | Rank filters raw MS/MS spectra by removing any peaks not in the top k scoring peaks within \+/\- 56 Da \\ |
| CLUST_RANK_FILTER \\ | any integer >0 \\ | \-1 | Rank filters clustered MS/MS spectra by removing any peaks not in the top k scoring peaks within \+/\- 56 Da \\ |
| PRM_RANK_FILTER \\ | any integer >0 | \-1 | Rank filters PRM spectra by removing any peaks not in the top k scoring peaks within \+/\- 56 Da |
| CORRECT_PM | yes/no \\ | no \\ | Correct MS/MS spectra parent mass. \\ |
| MIN_OVERLAP_AREA | 0.0 - 1.0 | 0.45 \\ | Minimum percentage of overlapping mass between two spectra to compute spectral alignments. Lower values allow for the detection of small overlaps but lead to longer run times; usually not set to less than 0.4. \\ |
| MIN_RATIO | 0.0 - 1.0 | 0.35 \\ | Minimum percentage of matched peak scores in a spectral alignment. \\ |
| MIN_PEAK_INT | any float > 0 | 50.0 | Minimum peak intensity in MS2 spectrum before MSCluster |
| MIN_MATCHED_PEAKS | Any integer >0 | 4 \\ | Minimum number of matched peaks in a spectral alignment. \\ |
| MAX_PVALUE | 0.0 - 1.0 | 0.05 \\ | Maximum p-value to accept spectrum/spectrum alignment. Default value is 0.05 (may be too strict for datasets with small number of spectra). \\ |
| FILTER_PRECURSOR_WINDOW\\ | 0/1 | 0 | Removes peaks with (-20,+15) Th of the theoretical precursor mass. |
| FILTER_TRIGS | yes/no \\ | yes \\ | Determines whether spectral alignments need to be confirmed by transitive closure. If set to "yes" then a spectral alignment between spectra A,B is only accepted if there are at least two other alignments A,C and B,C with consistent alignment offsets. Default is "yes", should be set to "no" for spectral networks projects. \\ |
| MIN_MATCHED_PEAKS_DB | Any integer >=4 | 6 \\ | Minimum number of matched peaks when aligning contig sequences against the FASTA database. \\ |