metaboigniter

whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any).

whether to disallow charge mismatches (Identical), allow to link charge zero (i.e., unknown charge state) with every charge state, or disregard charges (Any).

m/z tolerance (in ppm or Da)

Width of RT tolerance window (sec)

The maximal number of peaks/features to be considered per map. To use all, set to '-1'.

Unit of m/z tolerance

Number of partitions in m/z space

Never pair features with larger m/z distance (unit defined by 'unit')

Unit of the 'max_difference' parameter

Never pair features with a larger RT distance (in seconds).

false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state

Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.

Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.

Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)

m/z tolerance (in ppm or Da)

Width of RT tolerance window (sec)

possible negative adducts for adduct detection in the format of adduct:charge:probablity

possible positive adducts for adduct detection in the format of adduct:charge:probablity

Maximal possible charge

Minimal possible charge

Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge

Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.

Maximum allowed mass tolerance per feature. Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!

Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise. E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well.

Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!

Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)

Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').

Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)

Maximum allowed RT difference between any two features if their relation shall be determined

Unit of the 'max_difference' parameter

Prune the considered adduct transitions by transition probabilities.

If set to true, identification will be performed. Remember to set identification specific parameters

Set wether the MS2 collections have been done on all the MS1 data. If there is a separate MS2 file, set to separate

If set, the linking will be performed in parallel, see nr_partitions in linking

Polarity of the data

If set to true, requantification will be performed

Custom MultiQC yaml file containing HTML including a methods description.

Email address for completion summary.

Path to comma-separated file containing information about the samples in the experiment.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

If set, detected adduct will be used in identification

mz tolerance (ppm) for finding C13

rt tolerance for finding C13

If set, MS2Query will be run

If set SIRIUS will run

E-mail for your SIRIUS account.

Search structures in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

Password for your SIRIUS account.

If set, FingerID will be run. This has to be run together with run_sirius

If set, passatutto will be run

The number of formula candidates in the SIRIUS output

Minimum number of candidates in the output for each ionization. Set to force output of results for each possible ionization, even if not part of highest ranked results.

Search formulas in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

the iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts.

Disable recalibration of input spectra

Maximum allowed mass deviation in ppm for decomposing masses (ppm)

Maximum allowed mass deviation in ppm for decomposing masses in MS2 (ppm).If not specified, the same value as for the MS1 is used.

Name of the configuration profile

If set, SIRIUS will be run in parallel. See mgf_splitmgf_pyopenms parameter for segmentation

For running MS2 mapping in parallel set this higher than 1

Expected chromatographic peak width (in seconds).

Minimum signal-to-noise a mass trace should have.

Intensity threshold below which peaks are regarded as noise.

Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.

Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.

Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..

Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.

Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).

Allowed mass deviation (in ppm).

Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.

Enables dynamic re-estimation of m/z variance during mass trace collection stage.

Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)

Expected elution peak width in seconds, for smoothing (Gauss filter). Also determines the RT extration window, unless set explicitly via 'extract:rt_window'.

Alternative initial parameters for fitting through method of moments.

Maximum number of iterations for EMG fitting.

m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)

Number of isotopes to include in each peptide assay.

Type of elution model to fit to features