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Peak detection software tools | MS-based untargeted proteomics

In a typical proteomic experiment, a huge volume (e.g. 1 GB) of MS data is often generated. Each of MS spectra consists of two large vectors corresponding to mass to charge ratio (m/z) and intensity value, respectively. The first step in proteomic…
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…

PECAN
Desktop

PECAN PEptide-Centric Analysis

Detects peptides directly from data-independent acquisition (DIA) data without…

Detects peptides directly from data-independent acquisition (DIA) data without prerequisite spectral or retention time libraries. PECAN is a peptide-centric method used to build libraries directly…

DIA-Umpire
Desktop

DIA-Umpire

An open source Java program for computational analysis of data independent…

An open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. DIA-Umpire enables untargeted peptide and protein identification…

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…

mMass
Desktop

mMass

Covers a wide range of processing tasks such as import from various data…

Covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration.

SpiceHit
Desktop

SpiceHit

Identifies Capillary Electrophoresis Mass Spectrometry (CE-MS) analysis using…

Identifies Capillary Electrophoresis Mass Spectrometry (CE-MS) analysis using the selected ion monitoring (SIM) method. SpiceHit characterizes metabolite features by using migration times relative to…

MapQuant
Desktop

MapQuant

Quantifies comprehensively organic species detected in large MS datasets.…

Quantifies comprehensively organic species detected in large MS datasets. MapQuant treats an LC/MS experiment as an image and utilizes standard image processing techniques to perform noise filtering,…

Massifquant
Desktop

Massifquant

An open-source solution for Kalman filter (KF) isotope trace (IT) detection…

An open-source solution for Kalman filter (KF) isotope trace (IT) detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying…

MassSpecWavelet
Desktop

MassSpecWavelet

Identifies peaks by applying CWT-based pattern matching, which takes advantage…

Identifies peaks by applying CWT-based pattern matching, which takes advantage of the additional information present in the shape of the peaks. MassSpecWavelet can greatly enhance the estimation 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…

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…

PROcess
Desktop

PROcess

A package for processing protein mass spectrometry data.

A package for processing protein mass spectrometry data.

enviPick
Desktop
Web

enviPick

Sequential partitioning, clustering and peak detection of centroided LC-MS mass…

Sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML).

LCMS-2D
Desktop

LCMS-2D

A software tool for reliable data reduction of LC-MS proteomics data. LCMS-2D…

A software tool for reliable data reduction of LC-MS proteomics data. LCMS-2D can reliably reduce LC-MS spectra with multiple scans to a list of elution peaks, and subsequently to a list of peptide…

PrepMS
Desktop

PrepMS

A simple-to-use graphical tool that enables researchers to easily prepare…

A simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter…

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…

Cromwell
Desktop

Cromwell

An algorithm to process the spectra, denoising with the undecimated discrete…

An algorithm to process the spectra, denoising with the undecimated discrete wavelet transform (UDWT).

LIMPIC
Desktop

LIMPIC

A computational method for the detection of protein peaks from linear-mode…

A computational method for the detection of protein peaks from linear-mode MALDI-TOF data. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is…

findMF
Desktop

findMF find Molecular Features

Finds molecular features base functions and detects in 1D and 2D qTOF mass…

Finds molecular features base functions and detects in 1D and 2D qTOF mass spectrometry (MS) data. findMF is a header only library with good unit test coverage. It is composed of distinct parts:…

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