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Separate documentation is available for both [Molecular Networking Analysis|https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Analysis+Documentation] and [Cytoscape 2.8|https://bix-lab.ucsd.edu/display/Public/Cytoscape+2.8.X+Visualization+and+Analysis+Documentation] and [Cytoscape 3.2|https://bix-lab.ucsd.edu/display/Public/Cytoscape+3.2.X+Visualization+and+Analysis+Documentation]




h4. Data Analysis on GNPS

| {color:#000000}{*}Fragment Ion Mass Tolerance{*}{color} {color:#000000}*(FIMT)*{color} | {color:#000000}Parameters used for MS-Cluster, molecular networking, and MS/MS spectral library searches. For every group of MS/MS spectra being considered for clustering (consensus spectrum creation), this value specifies how much fragment ions can be shifted from their expected{color} {color:#000000}m{color}{color:#000000}/{color}{color:#000000}z{color} {color:#000000}values. Default value is ± 0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ± 2.0 Da for low-resolution instruments (ion traps, QqQ).{color} | 0.02 \\ |

{color:000000}Table showing the Da/ppm equivalent depending o{color}{color:000000}{_}n m{_}{color}{color:000000}/{color}{color:000000}{_}z{_}{color} {color:000000}range. Refer to it when selecting adjusting the Precursor Ion Mass Tolerance (PIMT) or Fragment Ion Mass Tolerance (FIMT) based on your experimental conditions.{color}

| | 2.0 Da | 0.5 Da | 0.1 Da | 0.05 Da | 0.03 Da | 0.025 Da | 0.02 Da | 0.0175 Da | 0.015 Da | 0.01 Da | 0.0075 Da |
| m/z 200 | 10000 ppm | 2500 ppm | 500 ppm | 250 ppm | 150 ppm | 250 ppm | 100 ppm | 87.5 ppm | 75 ppm | 50 ppm | 37.5 ppm |
| m/z 500 | 4000 ppm | 1000 ppm | 200 ppm | 100 ppm | 60 ppm | 49 ppm | 40 ppm | 35 ppm | 29 ppm | 20 ppm | 15 ppm |
| m/z 1000 | 2000 ppm | 500 ppm | 100 ppm | 50 ppm | 30 ppm | 25 ppm | 20 ppm | 17.5 ppm | 15 ppm | 10 ppm | 7.5 ppm |
| m/z 1500 | 1333 ppm | 333 ppm | 66 ppm | 33 ppm | 20 ppm | 16 ppm | 13 ppm | 11.6 ppm | 10 ppm | 6.6 ppm | 5.0 ppm |
| m/z 2000 | 1000 pm | 250 pm | 50 ppm | 25 ppm | 15 ppm | 12.5 ppm | 10 ppm | 8.75 ppm | 7.4 ppm | 5.0 ppm | 3.75 ppm |

h4. Advanced Network Options