Comparison of few data processing tools- A tabular view

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Tools for Metabolomics data processing and analysis

Table: comparison of main features
- Metaboanalyst Mzmatch MZmine2 MetAlign
Functionality Processing, analyzing, visualizing, and annotating high throughput metabolomics data Data processing pipeline for metabolomics LC-MS data mass-spectrometry data processing with the main focus on LC-MS data Untargeted metabolite identification data preprocessing of high throughput metabolomics data
Features Peak detection, Retention time correction, Peak alignment,

Base line filtering

Peak extraction, Retention time alignment, Filtering, Normalization, Derivative detection, Identification Peak detection,

Identification of peaks using online databases, and custom databases

alignment, peak-picking, and baseline corrections
Input format mzXML



MzXML, mzData, PeakML

mzML, mzXML




Input types NMR peak lists, binned spectra, MS peak lists, compound/concentration data 2D mass spectrometry dataThermoRAW MZmine 2 can read and process both unit mass resolution and exact mass resolution data (e.g. FTMS) in both continuous and centroided modes, including fragmentation (MSn) scans full scan nominal or accurate mass LC-MS and GC-MS data
Technology JSF, R-Bioconductor package(XCMS)data Java

Built on top of the peakML core library

Java Java
For what data LC-MS, GC-MS, NMR LC-MS LC-MS LC-MS,


Possibility to integrate into workflow mgt. system Yes

(provided the authors give R scripts)

yes yes not possible
Server Linux system Linux Linux Windows
Operating system Windows,

Linux, Mac


Linux, Mac


Linux, Mac

downloadable R scripts- Not available online yet yes yes yes
GUI yes GUI & command line GUI & command line yes
Web based yes Yes yes
Operating procedure data upload

processing normalization statistical analysis annotation summary report

raw data upload

Convert to peakML format processing normalisation analysis

Advantages Metaboanalyst provides its own metabolite and pathway identification tools

Small collection of R scripts that can be downloaded and reused (however, the scripts not readily available online yet

Modular application. Collection of small tools for the common processing tasks for LC-MS data. PeakML file format ( the tools can share their data output with the other software because of flexible format to store intermediate

data(extracted mass traces, matched sets of these, parameters, etc.)

MSn data support.Improved isotope pattern support, scatter plot visualization, peak list alignment based on the random sample consensus (RANSAC) algorithm

MZmine 2 can visualize the raw data together with peak picking and identification results, which is very useful for evaluating different peak detection methods.

Easy use of both GC/MS and LC/MS data.Direct conversion to and from manufacturer formats, as well as netCDF (network Common Data Form), Export of the result to manufacturer formats for visual inspection, Alignment at low mass and high mass resolutions
Limitations Metaboanalyst mostly depended on HMDB infrastructure, means that its coverage of plant and microbial metabolism is somewhat incomplete.Metaboanalyst requires users to perform some manual processing steps prior to uploading the data.

Steps such as phasing, baseline correction, referencing, peak detection and deconvolution must be manually checked by an experienced analyst to ensure the integrity of the results. System crashes if the input data is more than 50MB. Error message if the data upload takes more than 15 minutes.

MS/MS data support only. Cant read MSn data For now only centroid input data is supported NetCDF is not supported as it misses necessary meta-information

Direct injection data will not yield correct results

An important problem with MZmine is the possible misalignment of the internal standard. Since it is a prerequisite that the internal standard must be present in all samples with the same retention time/mass pair, other less selective ions than the most specific ion may need to be used for normalisation or no normalisation on an internal standard may be possible. Major disadvantage is metalign is highly closed software. No command line version.

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