slight change to documentation
@@ -43,7 +43,7 @@ It is worth mentioning that the link between the MS2 spectra, and the presumed p
ions from the MS2 fragmentation spectra from an abundant compound with a long chromatographic tail will often show up in the MS2 values of unrelated compounds, but whose precursor isolation window picks up ions from the original compound.
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-An experimental module which converts the MS2 similarity relationships exported from MZmine2 in CSV format into GraphML format suitable for viewing in the freely available graph manipulation software <a href="http://www.cytoscape.org">Cytoscape</a> is available on Github (<a href="https://github.com/photocyte/ms2_graph">https://github.com/photocyte/ms2_graph</a>).
+An experimental Python script which converts the MS2 similarity relationships exported from MZmine2 in CSV format into GraphML format suitable for viewing in the freely available graph manipulation software <a href="http://www.cytoscape.org">Cytoscape</a> is available on Github (<a href="https://github.com/photocyte/ms2_graph">https://github.com/photocyte/ms2_graph</a>).
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<h3>Method parameters</h3>
@@ -63,7 +63,8 @@ An experimental module which converts the MS2 similarity relationships exported
<dt>m/z tolerance</dt>
<dd>Allowable m/z difference for two ions to be considered identical, and therefore "matched".
Depends on the mass accuracy, precision, and resolution of the MS data. For data obtained on HRAM instruments, and when comparing within the same peaklist
- (aka the same experiment or LC/MS run), can be set to the mass precision of the instrument during that experiment (4e-4 m/z or ~1 PPM for Q-Exactive).</dd>
+ (aka the same experiment or LC/MS run), can be set to the mass precision of the instrument during that experiment (4e-4 m/z or ~1 PPM for Q-Exactive).
+ It is recommended that you set this value to the smallest range which reliably matches your ions of interest.</dd>
<dt>Minimum ion intensity to consider in MS2 comparison</dt>
<dd>Intensity threshold below which ions will be ignored</dd>
