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Peak alignment software tools | MS-based untargeted proteomics

Liquid chromatography-mass spectrometry is widely used for comparative replicate sample analysis in proteomics, lipidomics and metabolomics. Before statistical comparison, registration must be established to match corresponding analytes from run to…
OpenMS
Desktop

OpenMS

Allows to manage and analyse Liquid chromatography coupled to mass spectrometry…

Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such…

ptw
Desktop

ptw Parametric Time Warping

Aims to put corresponding features at the same locations. The algorithm…

Aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples…

MZmine
Desktop

MZmine

An open-source software tool for mass-spectrometry data processing, with the…

An open-source software tool for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the 2006 Bioinformatics publication, but…

msInspect
Desktop

msInspect

Allows to view mass spectrometry (MS1) data in an mzXML file. msInspect is An…

Allows to view mass spectrometry (MS1) data in an mzXML file. msInspect is An open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental…

SuperHirn
Desktop

SuperHirn

A tool to quantitatively analyze multi-dimensional LC-MS data in a label-free…

A tool to quantitatively analyze multi-dimensional LC-MS data in a label-free approach.

SpecArray
Desktop

SpecArray

Generates a peptide versus sample array from a set of Liquid…

Generates a peptide versus sample array from a set of Liquid Chromatography-Mass Spectrometry (LC-MS) data. SpecArray is a software suite that fulfills the important second step of the LC-MS approach…

IDEAL-Q
Desktop

IDEAL-Q

An automated analysis tool for label-free quantitative proteomics. IDEAL-Q…

An automated analysis tool for label-free quantitative proteomics. IDEAL-Q accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time…

GCalignR
Desktop

GCalignR

Contains functions to align peaks from gas chromatography (GC) and GC-mass…

Contains functions to align peaks from gas chromatography (GC) and GC-mass spectrometry (MS) data based on retention times and evaluate the resulting alignments. GCalignR, a user-friendly R package…

DISCO
Desktop

DISCO DIstance and Spectrum Correlation Optimization

Conducts alignments for two-dimensional gas chromatography time-of-flight mass…

Conducts alignments for two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS)-based metabolomics. DISCO uses Euclidean distances of two-dimensional retention times and…

Regression-base…
Desktop

Regression-based alignment methods

Permits a linear and non-linear retention time (rt) alignment of peak-picked…

Permits a linear and non-linear retention time (rt) alignment of peak-picked data in liquid chromatography and mass spectrometry (LC/MS) runs. Many alignment methods have been proposed in the…

CPM
Desktop

CPM Continuous Profile Models

This toolbox provides Matlab implementations of Continuous Profile Models (CPM)…

This toolbox provides Matlab implementations of Continuous Profile Models (CPM) for alignment and normalization of time series data.

MetPP
Desktop

MetPP METabolomics Profiling Pipeline

Analyzes metabolomics data generated from the 2D gas chromatography…

Analyzes metabolomics data generated from the 2D gas chromatography time-of-flight mass spectrometry (GCxGC-TOF MS) instrument. MetPP is able to recognize the concentration difference of the…

SIMA
Desktop

SIMA

Combines hierarchical pairwise correspondence estimation with simultaneous…

Combines hierarchical pairwise correspondence estimation with simultaneous alignment and global retention time correction. SIMA employs a tailored multidimensional kernel function and a procedure…

CowCoDA
Desktop

CowCoDA

Performs retention time alignment on set of peaks. CowCoDA combines mass…

Performs retention time alignment on set of peaks. CowCoDA combines mass chromatogram selection using CODA with a modified COW algorithm in order to take the local information in Liquid…

mSPA
Desktop

mSPA

Allows alignment of homogeneous data. mSPA is especially designed for…

Allows alignment of homogeneous data. mSPA is especially designed for two-dimensional gas chromatography mass spectrometry (GC × GC–MS). It employs the peak distance and the spectra similarity…

alignLCMS
Desktop

alignLCMS A Bayesian alignment model for LC-MS data analysis

A Bayesian alignment model for LC-MS data analysis. AlignLCMS provides…

A Bayesian alignment model for LC-MS data analysis. AlignLCMS provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of…

MALDIquant
Desktop

MALDIquant

An R package providing a complete and modular analysis pipeline for…

An R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in…

peak-grouping-a…
Desktop

peak-grouping-alignment

A direct matching peak alignment method for LC/MS data that incorporates…

A direct matching peak alignment method for LC/MS data that incorporates related peaks information (within each LC/MS run) and investigate its effect on alignment performance (across runs). The…

MbPA
Desktop

MbPA

Allows peak alignment on two-dimensional gas chromatography mass spectrometry…

Allows peak alignment on two-dimensional gas chromatography mass spectrometry (GCxGC-MS) Data. MbPA is able to deal with homogeneous and heterogeneous experimental data. It is based on a model peak…

SWPA
Desktop

SWPA Smith-Waterman Peak Alignment

Aligns homogeneous as well as heterogeneous peak data. SWPA is based on the…

Aligns homogeneous as well as heterogeneous peak data. SWPA is based on the Smith-Waterman local alignment in which the landmark peak selection and retention time transformation are not required. It…

HDP-Align
Desktop

HDP-Align Hierarchical Dirichlet Process Alignment

Aligns peaks via a hierarchical cluster model using both peak mass and…

Aligns peaks via a hierarchical cluster model using both peak mass and retention time. HDP-Align provides confidence values in the form of posterior probabilities allowing the user to distinguish…

PL
Desktop

PL PeakLink

Uses information in both the time and frequency domain as inputs to a…

Uses information in both the time and frequency domain as inputs to a non-linear support vector machine classifier. PeakLink offers the highest accuracy in various challenging test cases including…

MrR
Desktop

MrR

Analyzes the mass spectrometry (MS) data for baseline correction, denoising,…

Analyzes the mass spectrometry (MS) data for baseline correction, denoising, peak detection, peak alignment, peak normalization, and biomarker discovery. MrR is an R package for the Mass spectrometry…

Mass-Up
Desktop

Mass-Up

A software tool for the analysis of MALDI data. This is an application that…

A software tool for the analysis of MALDI data. This is an application that covers the whole process of MALDI data analysis, from data preprocessing to complex data analyses. Mass-Up incorporates the…

LWBMatch
Desktop

LWBMatch

An algorithm based on weighted bipartite matching. Unlike existing tools, which…

An algorithm based on weighted bipartite matching. Unlike existing tools, which search for accurate warping functions to correct chromatographic retention time shifts, it directly seeks a…

XCMS
Desktop

XCMS

An LC/MS-based data analysis approach which incorporates novel nonlinear…

An LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. The XCMS software reads and processes LC/MS data stored in…

GCAligner
Desktop

GCAligner

Performs a preliminary data comparison matrix of chemical data obtained by gas…

Performs a preliminary data comparison matrix of chemical data obtained by gas chromatography (GC) without mass spectrometry (MS) information. GCAligner is a computer program based on the comparison…

AMSRPM
Desktop

AMSRPM AMSRobust Point Matching

A package for the registration of either chromatograms or peak lists. AMSRPM…

A package for the registration of either chromatograms or peak lists. AMSRPM implements a variant of the Robust Point Matching algorithm that is tailored for the alignment of LC and LC/MS…

PEPPeR
Desktop

PEPPeR Platform for Experimental Proteomic Pattern Recognition

For the analysis of LC-MS data, GenePattern provides support for the algorithms…

For the analysis of LC-MS data, GenePattern provides support for the algorithms defined by PEPPeR, a Platform for Experimental Proteomic Pattern Recognition.

ChAMS
Web

ChAMS

Constructs optimal signal maps between mass spectrometry (MS) experiments and a…

Constructs optimal signal maps between mass spectrometry (MS) experiments and a practical application where these can be used to increase sensitivity and throughput. ChAMS was developed to rely on…

PeakMatch
Desktop

PeakMatch

It's separating double peaks, re-arranging turnover peaks, reducing…

It's separating double peaks, re-arranging turnover peaks, reducing general complexity, zooming into relevant peak areas and deleting irrelevant bands. The alignment method is robust against…

Chromaligner
Desktop

Chromaligner

Generates chromatogram alignment. Chromaligner aligns the chromatograms on…

Generates chromatogram alignment. Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW) for a collection of chromatograms and a set of defined peaks. It can be used…

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