Feature list import modules¶
mzTab import¶
Description¶
Feature list methods → Import feature list → mzTab
This module imports the contents of a mzTab file into a feature list. If links to raw data files are available in the mzTab file, these can automatically be imported together with the feature list.
Parameters¶
mzTab files¶
Names of the files to be imported
Import raw data files?¶
Optional parameter
If selected, raw data files will also be imported (if they are available).
If the raw data files are not available, empty raw data files will be generated by MZmine.
Warning
Please note that missing files may lead to issues with other modules that need access to the scan data.
mzTab-m import¶
Description¶
Feature list methods → Import feature list → mzTab
This module is highly similar to the previous one and imports the contents of a mzTab-m file into a feature list. If links to raw data files are available in the mzTab-m file, these can automatically be imported together with the feature list.
The raw data import searches for the files in the location provided in the mzTab-m file. If the files are not present, the search continues in the same folder as that of mzTab-m file. If the files are still not found, the import module checks if the files are present in compressed form (.gz or .zip). If no files are found after that, the empty rawFiles are created in the end.
Parameters¶
mzTab-m files¶
Names of mzTab-m files to be imported.
Import raw files too?¶
Optional parameter
If selected, raw data files will be imported if they are available. Files will be loaded from the msrun location defined in the mzTab-m file or from the folder containing the mzTab-m file. If the raw data files are not available, empty raw data files will be generated by MZmine.
Warning
Please note that missing files may lead to issues with other modules that need access to scan data.
csv¶
Description¶
Feature list methods → Import feature list → csv
This module imports features present from a csv file.
Warning
Imported csv file should follow a specific format described below.
This kind of format can be obtained by using xcms library in R to detect features using Centwave algorithm on a mzXML file.
The R code returns a list of features with following columns which can be exported to a csv file to be used as an import for this module. Column Numbering starts from 0, and 0th column is ignored.
| Column Name | Column No. |
|---|---|
| peak_mz | 1 |
| mzMin | 2 |
| mzMax | 3 |
| peak_rt | 4 |
| rtMin | 5 |
| rtMax | 6 |
| maxO | 9 |
where peak_mz - feature m/z value, peak_rt - feature retention time value, max 0 - intensity value.
Warning
To use this module, a user has to input the raw data file, which was used to generate peakList from the R code.
Example R code that generates the csv file
mzfile <- system.file("standards.mzXML")
library(xcms)
mzraw <- readMSData(files = mzfile, mode = "onDisk")
cpw <- CentWaveParam(ppm = 15, peakwidth = c(5,20), snthresh = 10)
mzData <- findChromPeaks(object = mzraw, param = cpw)
featurelist <- as.data.frame(xcms::chromPeaks(mzData))
write.csv(featurelist, "featureListFile.csv")
References¶
Quote
- Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical chemistry. 2006 Feb 1;78(3):779-87. DOI: 10.1021/ac051437y
Parameters¶
csv¶
CSV files in the desribed format to import
Raw data files¶
Raw data files that were used to generate imported feature lists.