SPS docs - analysis

compared with
Version 88 by Seungjin Na
on Jul 18, 2015 21:03.

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| ALIGNGF_MAX_PVALUE \\ | 0.0~1.0 | 1.0E-10 | Maximum AlignGF p-value to accept spectrum/spectrum alignment. Recommendation: 1.0E-10 \\ |
| MAX_PM_NUM_COMPONENT \\ | Any integer >=0 \\ | 0 | If>0, the number of unique masses of precursor ions in a single component should be equal to or less than the specified value. \\ |
| FILTER_PAIR_EDGE_FDR | 0.0~1.0 \\ | 0.01 | Retain only pairs at the specified FDR. Requirement: MSGF-DB PSM file. |
| FILTER_PAIR_EDGE_FDR | 0.0~1.0 \\ | 0.01 | Retain only pairs at the specified FDR. Requirement: MSGF-DB PSM file, where Scan# column should be matched to indice of specs_ms.mgf |
| REMOVABLE_BAD_CLUSTER_SIZE \\ | Any integer >=0  \\ | 0 | If>0, then try to remove repeated low-quality spectra of the same peptide even after ms-clustering. Only the clusters whose sizes are less than or equal to the specified value would be removed. \\ |

h4. Optional FT CID, HCD or ETD Parameters