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Feature list export modules

This section describes general format export modules. For the description of export modules for the specific software, please, refer to Data export to other software.

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CSV

Description

Feature list methods → Export feature list → CSV

This module allows to export obtained feature lists to csv (comma-separated values) file format.

Parameters

Field separator

Character(s) used to separate fields in the exported file. "," by default.

Identification separator

Character(s) used to separate multi object columns in the exported file. ";" by default.

Remove empty columns

Optional parameter

Removes empty columns during data export.

Filter rows

Allows user to export only those rows that have associated MS/MS data or are annotated.

CSV (legacy MZmine 2)

Description

Feature list methods → Export feature list → CSV (legacy MZmine 2)

This module is a legacy module from MZmine2 and, similarly to the previously described module, exports the contents of the feature list(s) into a csv file, which can later be processed by MS Excel or other tools. The produced CSV files cannot be imported back to MZmine. Missing values such as heights and areas of undetected features are exported as 0.

Parameters

Filename

Name of file where the exported data is saved

Field separator

Columns in the new CSV file will be separated by this character (coma by default)

Export common elements

Which row elements (such as row ID, row retention time, or best ion annotation) from the feature list will be exported

Export data file elements

Which feature elements (such as feature status, name, or tailing factor) will be exported.

Export quantitation results and other information

Optional parameter

If checked, all feature-associated data will be exported.

Identification separator

Character to separate multiple identification results (if they are available) for a feature.

Filter rows

Allows user to export only those rows that have associated MS/MS data or are annotated.

Export all annotations to CSV

Description

Feature list methods → Export feature list → Export compound annotations to csv

Export all annotations from spectral library matching, local compound DB CSV matching, and others.

Parameters

Filename

Base file name of all annotation file (Use {} to fill in the feature list name when exporting multiple feature lists at once).

Top N per method

Export the top N annotations per annoation method.

Venn diagram export

Description

Feature list methods → Export feature list → Venn diagram export

Exports a feature list to a csv that can be plotted as a venn diagram by other software such as VennDis.

Parameters

Directory

Choose a directory to export the feature list to.

Export gap filled as detected

Optional parameter

If checked, gap filled features will be exported as detected, otherwise they will be marked as undetected.

mzTab export

Description

Feature list methods → Export feature list → mzTab

This module exports the contents of the feature list into a mzTab file, which can later be processed by other tools.

Parameters

Feature lists

Name of the feature list(s) to be exported.

Filename

Name of file where the exported data is saved.

Include all peaks

Optional parameter

If selected, the features with unknown identity will also be exported to the mzTab file.

mzTab-m export

Description

Feature list methods → Export feature list → mzTab-m

This module exports the contents of the feature list into a mzTab-m file, which can later be processed by other tools.

Parameters

Feature lists

Name of the feature list(s) to be exported

Filename

Name of file where the exported data is saved

Include all peaks

Optional parameter

If selected, the features with unknown identity will also be exported to the mzTab file.

SQL export

Description

Feature list methods → Export feature list → SQL database

This module allows direct export of the feature lists into MySQL or PostgreSQL database servers. If you would like to use another database then please add its JDBC driver (jar file) to the MZmine lib/ folder.

Parameters

Feature lists

Name of the feature list(s) to be exported

JDBC connection string

Identification of the database according to the JDBC standard. For example:

jdbc:mysql://localhost/dbname?dbname=sqluser&password=sqluserpw

Database table

Name of the table, into which data will be exported.

Export columns

The mapping between the database table columns (“Table column”) and MZmine data types (“Export data type”). For some data types an additional value (“Export value”) must be specified, such as for the “Constant value” type.

Export empty feature list

Optional parameter

If selected, an empty feature list will be exported. All columns, other than raw data file and constants, will be assigned null values.

MSP Export

Description

Feature list methods → Export feature list → MSP file (ADAP)

This module exports fragmentation spectra of peaks in the feature list into MSP format file. In addition to the spectra, the following feature characteristics are saved into the file:

  • Name Name of the peak as displayed in the peak list
  • DB# Row number in the peak list
  • RT Optional Retention time of a feature
  • ANOVA_P_VALUE (optional) P-value calculated by the module Data analysis -> One-way ANOVA Test
  • Num Peaks Number of peaks in the spectrum

Parameters

Feature lists

Name of the feature list(s) to be exported

Filename

Name of file where the exported data is saved

Add retention time

If selected, each MSP record will contain feature's retention time.

Add ANOVA p-value (if calculated)

If selected, each MSP record will contain the One-way ANOVA p-value if such p-value is present

Integer m/z

If selected, fractional m/z values will be rounded to the closest integer, and a new intensity will be calculated based on the merging mode:

  • Maximum: new intensity is the maximum of merged intensities,
  • Sum: new intensity is the sum of merged intensities.

MGF Export

Description

Feature list methods → Export feature list → MGF file (ADAP)

This module exports fragmentation spectra of features in the feature list into MGF (Mascot Generic Format) format file.

Parameters

Feature lists

Name of the feature list(s) to be exported

Filename

Name of file where the exported data is saved

Representative m/z

Choose the reprezentative m/z values of a cluster. The available options are: - As in feature table, - Highest m/z, - Or maximum intensity.

Fractional m/z values

Optional parameter

If selected, fractional m/z values will be saved. If not, all fractional m/z values will be rounded to the closest integer.

Warning

In case of rounding to integer, the corresponding features will be merged.

Integer m/z

When features are merged, the resulting elution profile is calculated by one of the following rules: - Maximum. In the resulting elution profile, the intensity at retention time t is the maximum of the intensities at t across the merging elution profiles. - Sum. In the resulting elution profile, the intensity at retention time t is the sum of the intensities at t for all merging elution profiles.

Export feature network to csv

Description

Feature list methods → Export feature list → Export feature network to csv

Export results from correlation/MS annotation as networks to csv.

Parameters

Filename

Base file name of all edge files (Use {} to fill in the feature list name when exporting multiple feature lists at once).

Export row relationships

Optional parameter

Export all relationships of different rows to files. The relationships that can be exported include: - MS1 feature correlation - Ion identity network - MS2 cosine similarity - MS2 neutral loss cosine similarity - MS2 modified cosine similarity (GNPS)

Combine to one file

Optional parameter

If chosen, all output is combined into one file. Otherwise, a separate file is exported per each relationship type.

Export IIN edges

Optional parameter

Export all edges of Ion Identity Networks (IIN).

Export IIN relationship edges

Optional parameter

Export relationships between Ion Identity Networks (IIN).

Filter rows

Limit the exported rows to those with MS/MS data and/or annotated rows.

Spectral library batch generation

Description

Feature list methods → Export feature list → Spectral library batch generation

This module allows to generate spectral library using metadata sheet.

Parameters

Feature lists

Name of the feature list(s) to be exported.

Export file

Name of a local library file where the exported data is saved.

Export format

File format for the export. Available options: - MZmine json (recommended), - And NIST msp.

Metadata

Metadata for all entries.

Metadata setup

In this dialog user can setup all dataset-related data, including the decription, ID (either from MassIVE, MetaboLights, or Metabolomic Workbench), specifications of the instrument, information on researchers involved in the dataset creation, and ion mode.

Metadata setup

m/z tolerance (merging)

Optional parameter

The tolerance used to group signals during merging of spectra. If selected, spectra from different collision energies will be merged.

Handle chimeric spectra

Optional parameter

Options to identify and handle chimeric spectra with multiple MS1 signals in the precursor ion selection.

Handle chimeric spectra setup

This dialog allows to set parameters for handling chimeric spectra. The spectrum detected as chimeric will be flagged if this option is chosen.

Chimeric spectra setup

Quality parameters

Quality parameters for MS/MS spectra to be exported to the library.

Quality parameters spectra setup

The following dialog allows to set the criteria for the MS/MS export to the library, such as minimum number of signals, percentage of explained signals or intensity, etc.

Quality parameters

Robin Schmid, omokshyna


Last update: April 6, 2023 09:55:53