1) Upload your data

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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. For more information about all possible data formats, please read the MS Peaks to Paths FAQs.

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
                                

2) Try our example data

IBD
Three columns (m.z, p.value, t.score)
Example peak list data created from a subset of pediatric IBD stool samples (12 IBD patients and 12 healthy controls) obtained from the Integrative Human Microbiome Project Consortium (iHMP). This data was collected using a Q-Exactive Plus Orbitrap MS (negative ion mode).
ImmuneCell
One column (m.z ranked by p.value)
Example ordered peak list data obtained from untargeted metabolomics of human monocyte-derived dendritic cells under stimulation by a strain of yellow fever virus (YF17D, vaccine strain), collected using an Orbitrap LC-MS (positive ion mode).
Macrophages
Four columns (m.z, p.value, t.score, mode)
Example peak list from mice alveolar macrophages in lungs, with or without mTOR knock-out (details). This data was obtained using an Orbitrap LC-MS (C18 negative ion mode and HILIC positive ion mode)
IBD 2
Four columns (m.z, p.value, t.score, rt)
Example peak list data created from a subset of pediatric IBD stool samples (12 IBD patients and 12 healthy controls) obtained from the Integrative Human Microbiome Project Consortium (iHMP). This data was collected using a Q-Exactive Plus Orbitrap MS (negative ion mode).
ImmuneCell Table
Peak intensity table
Example peak intensity table from KO experiment of dendritic cells and epithelial cells treated in DSS.
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