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Tutorial

1. Keywords

Enter some keywords in the search box, then click "search" button.

Displays search results much with words entered.

2. Detail

Click "ToMMo Compound ID" or "Name" in Item Table.

Move to the compound (metabolite/protein) detail page.

Metabolite

Protein

3. Correlation Network viewer

Correlation tables can be visualized as networks. Users can interactively explore correlation network. Click "View as network" button to switch to network view.


Terms

Mode of Metabolites [MS]

  • GMet: Global metabolomics, Methods of researching metabolites by untargeted metabolic profiling
  • C18: Analytical condition of reverse phase mode using octa decal silly (ODS, C18) column by LC-MS
  • HILIC: Analytical condition of normal phase mode using Hydrophilic interaction chromatography (HILIC) column by LC-MS
  • Pos: Positive ion mode
  • Neg: Negative ion mode

Correlation Tables

Table

In the correlation tables correlations are showed of |rs| > 0.2.

  • rank: rank of descending order of correlation coefficient rs
  • rs: Spearman's correlation coefficient between two metabolites
  • -log10(p): "p" is p-value of correlation coefficient

Rank Plot

Plot of all descending ordered rs.

Peptide Information of Proteins

  • Start: Index of the N-terminal amino acid of the peptide in the protein sequence
  • End: Index of the C-terminal amino acid of the peptide in the protein sequence
  • Sequence: Amino acid sequence of the observed peptide
  • rsID: dbSNP ID(s) of the non-synonymous SNVs within the peptide sequence. Detailed information of the SNVs is available in the iJGVD website, which will appear by clicking the hyperlinks on the rsIDs.
  • Mutation: Amino acid mutation(s) corresponding to the rsIDs.
  • Allele: The allele type of the peptide sequence. REF and ALT indicate the reference and alternative alleles, respectively.
  • m/z: The ratio of the molecular-weight and charge of the peptide.
  • Charge: Charge of the peptide
  • Modifications: Chemical modifications observed in the peptide

Download

FIle Details

Users can download the summary of search results in a tab-delimited text format. The downloaded fields are:

  • ToMMo compound ID, compound name, notes, category
  • subject number, mean, SD, CV, and detection rate range in Proteins,for all, male, and female
  • link information for other database, and m/z, retention time, mode in Metabolites [MS]

Contents of file

  • The firstr line: Version of the data
  • The second line: Download date
  • Third row: Item name
  • Fourth row after: Search results

Help

ToMMo Compound ID rule

ToMMo Compound IDs have the form like TCx123456. The first two letter, TC, indicates the ID is ToMMo Compound ID (TC-ID). The following one letter identifies the data source. Now, we provide four kinds of data: (P) proteome by MS, (N) NMR, (Z) MS metabolome in HILIC mode, and (O) MS metabolome in C18 mode. The last six digits are unique number for a compound in each data source. In MS metabolome, data source can be further divided into positive mode and negative one. If the 6 digits is less than 500,000, a compound with the number was identified by negative mode. Otherwise, the compound was found by positive mode.

Name of Metabolites [MS]

The separator “||” means that multiple candidates were identified with one feature, which have similar retention time on the chromatogram, m/z and fragment ions by collision-induced dissociation.