Metabolite identification is the current bottleneck in non-targeted metabolomics. While tandem MS data allows to identify metabolites to a certain degree, but orthogonal information such as retention time is required to achieve higher confidence. in silico analysis of tandem MS data is fairly advanced, but only marginal improvements for the prediction of retention times have been made. One reason is missingness of comprehensive training data.
This repository contains training data for retention time prediction. Data was collected from different sources, such as PredRet, Metabolights, primary literature and own data sets.
If you would like to submit a retention time data directly via GitHub, but please first request an ID for your data via eMail to Dr. Michael Witting eMail. An example dataset and Excel template can be found here. Data is typically submitted via a fork and pull request. Upon pull request a GitHub action workflow is triggered for checking data quality and performing standardization.
The retention time data has to contain the following columns
- id
- name
- formula
- rt
- pubchem.cid
- pubchem.smiles.isomeric
- pubchem.smiles.canonical
- pubchem.inchi
- pubchem.inchikey
- id.chebi
- id.hmdb
- id.lipidmaps
- id.kegg
The substance id consists of the data id (e.g. 0001) concatenated to a running number for each metabolite by an underscore. An example would be 0001_00001. This allows to identify each individual substance throughout the entire dataset. Minimum one chemical identifier is required to obtain the substance structure. Pubchem CIDs are prefered. If the subtance is not found in a database yet, please add the SMILES of the substance in the field pubchem.smiles.isomeric. Standardization of SMILES and generation of InChI and InChIKey is performed automatically and data is transferred to a corresponding subfolder in the processed_data folder.
The following information helps to classify and describe the employed chromatogrpahic system. Please use standardized names as found in Resources/usp_classification.
| name | information |
|---|---|
| column.name | Standardized name according to list found Resources/usp_classification |
| column.usp.code | USP code of column according to list found Resources/usp_classification |
| column.length | Length of column in mm |
| column.id | Inner diameter of column in mm |
| column.particle.size | Particle size in um |
| column.temperature | Temperature of column in °C |
| column.flowrate | Flowrate in mL/min |
Beside the chromatographic column data on eluents is encoded in the metadata table. This contains information on solvents and additives used.
At the current stage only up to 4 solvent channels are available. Practically, all common cases are covered with ths. If additional solvents are required, they can be added at any time. Base composition of solvents is recored in volume-%. Values for all solvents for one eluent should add up to 100%.
The following table summarizes all currently used solvents, their abbrevation used, as well as the naming of the variable for the eluents A-D.
| name | abbrev | unit | A | B | C | D |
|---|---|---|---|---|---|---|
| water | h2o | % | eluent.A.h2o | eluent.B.h2o | eluent.C.h2o | eluent.D.h2o |
| methanol | meoh | % | eluent.A.meoh | eluent.B.meoh | eluent.C.meoh | eluent.D.meoh |
| acetonitrile | acn | % | eluent.A.acn | eluent.B.acn | eluent.C.acn | eluent.D.acn |
| 2-propanol | iproh | % | eluent.A.iproh | eluent.B.iproh | eluent.C.iproh | eluent.D.iproh |
| hexane | hex | % | eluent.A.hex | eluent.B.hex | eluent.C.hex | eluent.D.hex |
| chloroform | chcl3 | % | eluent.A.chcl3 | eluent.B.chcl3 | eluent.C.chcl3 | eluent.D.chcl3 |
| dichloromethane | ch2cl2 | % | eluent.A.ch2cl2 | eluent.B.ch2cl2 | eluent.C.ch2cl2 | eluent.D.ch2cl2 |
| heptane | hept | % | eluent.A.hept | eluent.B.hept | eluent.C.hept | eluent.D.hept |
| acetone | acetone | % | eluent.A.acetone | eluent.B.acetone | eluent.C.acetone | eluent.D.acetone |
| additive | abbrev | unit | A | B | C | D |
|---|---|---|---|---|---|---|
| formic acid | formic | % | eluent.A.formic | eluent.B.formic | eluent.C.formic | eluent.D.formic |
| acetic acid | acetic | % | eluent.A.acetic | eluent.B.acetic | eluent.C.acetic | eluent.D.acetic |
| trifluoroacetic acid | trifluoroacetic | % | eluent.A.trifluoroacetic | eluent.B.trifluoroacetic | eluent.C.trifluoroacetic | eluent.D.trifluoroacetic |
| phosphoric acid | phosphor | % | eluent.A.phosphor | eluent.B.phosphor | eluent.C.phosphor | eluent.D.phosphor |
| ammonium acetate | nh4ac | mM | eluent.A.nh4ac | eluent.B.nh4ac | eluent.C.nh4ac | eluent.D.nh4ac |
| ammonium formiate | nh4form | mM | eluent.A.nh4form | eluent.B.nh4form | eluent.C.nh4form | eluent.D.nh4form |
| ammonium carbonate | nh4carb | mM | eluent.A.nh4carb | eluent.B.nh4carb | eluent.C.nh4carb | eluent.D.nh4carb |
| ammonium bicarbonate | nh4bicarb | mM | eluent.A.nh4bicarb | eluent.B.nh4bicarb | eluent.C.nh4bicarb | eluent.D.nh4bicarb |
| ammonium fluoride | nh4f | mM | eluent.A.nh4f | eluent.B.nh4f | eluent.C.nh4f | eluent.D.nh4f |
| ammonium hydroxide | nh4oh | mM | eluent.A.nh4oh | eluent.B.nh4oh | eluent.C.nh4oh | eluent.D.nh4oh |
| triethylamine | trieth | mM | eluent.A.trieth | eluent.B.trieth | eluent.C.trieth | eluent.D.trieth |
| tripropylamine | triprop | mM | eluent.A.triprop | eluent.B.triprop | eluent.C.triprop | eluent.D.triprop |
| tributylamine | tribut | mM | eluent.A.tribut | eluent.B.tribut | eluent.C.tribut | eluent.D.tribut |
| N,N-dimethylhexylamine | nndimethylhex | mM | eluent.A.nndimethylhex | eluent.B.nndimethylhex | eluent.C.nndimethylhex | eluent.D.nndimethylhex |
Please indicate the starting end condition of the gradient by specifying the proportion of each eluent in %.
gradient.start.A gradient.start.B gradient.start.C gradient.start.D gradient.end.A gradient.end.B gradient.end.C gradient.end.D
Different ways to prepare solvent and gradients are used. For example eluents can be premixed or mixed via the solvent delivery system. A simple example shall illustrate this:
System 1:
Eluent A: 100% H2O + 0.1% formic acid
Eluten B: 100% ACN + 0.1% formic acid
The gradient starts from 95% A and 5% B and is increased linear to 5% A and 95% B in 10 minutes
System 2:
Eluent A: 95% H2O / 5% ACN + 0.1% formic acid
Eluten B: 5% H2O / 95% ACN + 0.1% formic acid
The gradient starts from 100% A and 0% B and is increased linear to 0% A and 100% B in 10 minutes.
The difference between the two systems is that the second system uses premixed eluents, while the first system uses the solvent delivery system to mimic the same mixing. However, nominally the two systems deliver the same gradient.
Using the metadata notation so far would flag them as two different systems for prediction of retention times. To overcome this issue the "true" gradient starting and ending conditions are calculated based on the solvent composition of the different eluents and the gradient conditions.
| solvent | abrev | unit | gradient start | gradient end |
|---|---|---|---|---|
| water | h2o | % | gradient.start.h2o | gradient.end.h2o |
| methanol | meoh | % | gradient.start.meoh | gradient.end.meoh |
| acetonitrile | acn | % | gradient.start.acn | gradient.end.acn |
| 2-propanol | iproh | % | gradient.start.iproh | gradient.end.iproh |
| hexane | hex | % | gradient.start.hex | gradient.end.hex |
| chloroform | chcl3 | % | gradient.start.chcl3 | gradient.end.chcl3 |
| dichloromethane | ch2cl2 | % | gradient.start.ch2cl2 | gradient.end.ch2cl2 |
| heptane | hept | % | gradient.start.hept | gradient.end.hept |
| acetone | acetone | % | gradient.start.acetone | gradient.start.acetone |
| additive | abbrev | unit | gradient start | gradient end |
|---|---|---|---|---|
| formic acid | formic | % | gradient.start.formic | eluent.B.formic |
| acetic acid | acetic | % | eluent.A.acetic | eluent.B.acetic |
| trifluoroacetic acid | trifluoroacetic | % | eluent.A.trifluoroacetic | eluent.B.trifluoroacetic |
| phosphoric acid | phosphor | % | eluent.A.phosphor | eluent.B.phosphor |
| ammonium acetate | nh4ac | mM | eluent.A.nh4ac | eluent.B.nh4ac |
| ammonium formiate | nh4form | mM | eluent.A.nh4form | eluent.B.nh4form |
| ammonium carbonate | nh4carb | mM | eluent.A.nh4carb | eluent.B.nh4carb |
| ammonium bicarbonate | nh4bicarb | mM | eluent.A.nh4bicarb | eluent.B.nh4bicarb |
| ammonium fluoride | nh4f | mM | eluent.A.nh4f | eluent.B.nh4f |
| ammonium hydroxide | nh4oh | mM | eluent.A.nh4oh | eluent.B.nh4oh |
| triethylamine | trieth | mM | eluent.A.trieth | eluent.B.trieth |
| tripropylamine | triprop | mM | eluent.A.triprop | eluent.B.triprop |
| tributylamine | tribut | mM | eluent.A.tribut | eluent.B.tribut |
| N,N-dimethylhexylamine | nndimethylhex | mM | eluent.A.nndimethylhex | eluent.B.nndimethylhex |