The Molecular Weight Tolerance refers to the ppm used for matching m/z features to compounds.

Use Generic if the data is formatted as a generic peak table. Note that if retention times are included, they must be formatted with two underscores between the m/z and retention time:

Sample              VT_150821_065.cdf       VT_150821_083.cdf
Group               healthy                 healthy
376.3808__0.93      119306.8796991          181692.0970101
135.1020__0.98      196722.430865503        337410.3473859
374.8815__0.59      409570.3544994          514658.461539
86.0603__2.15       1087129.323483          2038021.41222857
142.9618__1.35      638567.840138999        549900.622946999
129.0663__1.97      21840649.9192819        4237026.934809
                                    

The MS Peaks to Pathways module also supports the output directly from MZmine.

The Molecular Weight Tolerance refers to the ppm used for matching m/z features to compounds.

When primary ions are enforced, mz matches to compounds must contain a primary ion to be considered valid. Primary ions considered are 'M+H[1+]', 'M+Na[1+]', 'M-H2O+H[1+]', 'M-H[-]', 'M-2H[2-]', 'M-H2O-H[-]', 'M+H [1+]', 'M+Na [1+]', 'M-H2O+H [1+]', 'M-H [1-]', 'M-2H [2-]', and 'M-H2O-H [1-]'. Note this is only used in Version 2.

Mummichog requires p.values and GSEA requires t.scores for peak ranking purposes. You can upload your data in a tab-delimited text file (.txt) format. For single mode, for Version 1, a complete dataset contains three columns with specific names - m.z, p.value, and t.score. While for Version 2, a complete dataset contains four columns with specific names - m.z, p.value, t.score and r.t. For mixed mode, for Versions 1 and 2, your last column ("mode") must indicate whether the m.z's are positive or negative. Please see below for an example (mixed mode). Note that you can use fold change values instead of t.scores.

m.z             p.value                 t.score     mode
304.2979	1.0153771115e-10	14.7179316191   negative
177.1024	1.61647122234e-10	14.2666000207   negative
345.0277	1.71651483296e-10	-14.2091952724  positive
491.0325	1.83359804763e-10	-14.1463478332  positive
258.0048	2.16851438688e-10	-13.987636322   positive
483.1205	2.21510885538e-10	-13.9676335843  positive
694.9937	2.81091747637e-10	-13.7451720928  negative
270.9767	3.26786548614e-10	13.6060704804   positive
                                    

You must upload a text file which containing the potential chemical annotation for the MS peaks.

There are two formats for compound lists:

• A compounds list generated by Spectra Processing Module directly. This option contains the same rows of compounds as the peak list (See 2nd example, COVID-19 dataset);
• A compound list containing multiple rows whose number is different from the peak list. But, the first column must be the row index corresponding to the peak list. (See 1st example, Human Islet dataset).