Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Label-free protein quantification software tools | MS-based untargeted proteomics

There is a great interest in reliable ways to obtain absolute protein abundances at a proteome-wide scale. To this end, label-free LC-MS/MS quantification methods have been proposed where all identified proteins are assigned an estimated…
MaxQuant
Desktop

MaxQuant

A quantitative proteomics software package designed for analyzing large…

A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. MaxQuant is specifically aimed at high-resolution MS data. Several labeling techniques as well as…

LFQbench
Desktop

LFQbench Label-Free Quantification bench

An open source R package for the automated evaluation of label-free…

An open source R package for the automated evaluation of label-free quantification performance. The evaluation bases on the interpretation of the quantitative analysis results of hybrid proteome…

Census
Desktop

Census

A mass spectrometry data analysis tool for peptide/protein quantification. New…

A mass spectrometry data analysis tool for peptide/protein quantification. New features for analysis of isobaric labeling, such as Tandem Mass Tag (TMT) or Isobaric Tags for Relative and Absolute…

moFF
Desktop

moFF modest Feature Finder

An operating system relative quantification algorithm that scales to enable…

An operating system relative quantification algorithm that scales to enable quantitative analysis of very large mass-spectrometry-based proteomics data sets. The key benefits of moFF are (i) its OS…

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…

PEAKS
Desktop

PEAKS

Identifies peptides from a sequence database with tandem mass spectrometry…

Identifies peptides from a sequence database with tandem mass spectrometry data. PEAKS employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve both the speed…

ProStaR
Desktop

ProStaR

Provides a graphical user interface (GUI) interface for DAPAR. ProStaR is an R…

Provides a graphical user interface (GUI) interface for DAPAR. ProStaR is an R package that relies on Shiny technology to dynamically build web-based GUI to DAPAR functionalities. This plugin is…

DAPAR
Desktop

DAPAR Differential Analysis of Protein Abundance with R

Contains a collection of functions for the visualisation and the statistical…

Contains a collection of functions for the visualisation and the statistical analysis of proteomic data. DAPAR is an R package that gather in a single package, all the necessary statistical routines…

ProRata
Desktop

ProRata

Performs label-free quantification and isobaric chemical labeling…

Performs label-free quantification and isobaric chemical labeling quantification in addition to metabolic labeling quantification. ProRata is a versatile informatics system that enables…

APEX…
Desktop

APEX Quantitative Proteomics Tool

Provides a simple means to quickly derive hundreds to thousands of protein…

Provides a simple means to quickly derive hundreds to thousands of protein abundance values from standard liquid chromatography-tandem mass spectrometry proteomics datasets. The APEX tool provides a…

PIQED
Desktop
Progenesis QI
Desktop

Progenesis QI

Allows to analyze small molecule concerning liquid chromatography-mass…

Allows to analyze small molecule concerning liquid chromatography-mass spectrometry (LC-MS) data. Progenesis QI includes a search engine named Metascope. The characteristics of this tool (peak…

proBAMtools
Desktop

proBAMtools

Performs various analyses based on the proBAM files. proBAMtools includes…

Performs various analyses based on the proBAM files. proBAMtools includes functions for genome-based proteomics data interpretation, protein and gene inference, count-based quantification, and data…

MSQuant
Desktop

MSQuant

Allows visualization and validation of peptide identification results directly…

Allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass…

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…

MSqRob
Desktop

MSqRob

Allows a user to do quantitative protein-level statistical inference on liquid…

Allows a user to do quantitative protein-level statistical inference on liquid chromatography-mass spectrometry (LC-MS) proteomics data. MSqRob is a R package with a Shiny App that provides a…

SPLICIFY
Desktop

SPLICIFY

Identifies differentially expressed splice variants on RNA and protein level.…

Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative…

GProX
Desktop

GProX

A freely available complete software platform for comprehensive and integrated…

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets. GProX requires no special bioinformatics training, as all…

DanteR
Desktop

DanteR

A graphical R package that features extensive statistical and diagnostic…

A graphical R package that features extensive statistical and diagnostic functions for quantitative proteomics data analysis, including normalization, imputation, hypothesis testing, interactive…

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,…

aLFQ
Desktop

aLFQ

Supports the commonly used absolute label-free protein abundance estimation…

Supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling…

MassChroQ
Desktop

MassChroQ Mass Chromatogram Quantification

A versatile software that performs LC-MS data alignment and peptide…

A versatile software that performs LC-MS data alignment and peptide quantification by peak area integration on extracted ion chromatograms. MassChroQ is suitable for quantification with or without…

HiQuant
Desktop

HiQuant

Enables the rapid post-quantification analysis of large-scale mass spectrometry…

Enables the rapid post-quantification analysis of large-scale mass spectrometry (MS)-based proteomics datasets. HiQuant is a high-throughput protein quantification analysis tool. It implements a…

msVolcano
Web

msVolcano

A web application for the visualization of label-free mass spectrometric data.…

A web application for the visualization of label-free mass spectrometric data. msVolcano is optimized for the output of the MaxQuant data analysis pipeline of interactomics experiments and generates…

MaxReport
Desktop

MaxReport

An enhanced proteomic result reporting tool for MaxQuant, which is widely used…

An enhanced proteomic result reporting tool for MaxQuant, which is widely used in various types of proteomic studies such as in peptide identification, modification assignment, isotope labelling…

FlashLFQ
Desktop

FlashLFQ

Detects and quantifies chromatographic peaks. FlashLFQ is an open-source…

Detects and quantifies chromatographic peaks. FlashLFQ is an open-source application that enables delaying chromatographic peak detection. It reports either apex or integrated intensity of each peak.…

REQUIEM
Desktop

REQUIEM RElative QUantitation Inferred by Evaluating Mixtures

Allows users to work on relative quantitation. REQUIEM is a program that…

Allows users to work on relative quantitation. REQUIEM is a program that provides information about the quality of the data without employing replicates, standards, or assumptions regarding the…

Specter
Desktop

Specter

Identifies and quantifies spectral library members within data-independent…

Identifies and quantifies spectral library members within data-independent acquisition (DIA) data. Specter can analyze DIA-type data from any instrument vendor and acquisition scheme. This tool…

iMPAQT
Desktop

iMPAQT in vitro proteome-based MRM for Protein Absolute QuanTification

Permits measurement of the absolute abundance of any human protein in a given…

Permits measurement of the absolute abundance of any human protein in a given pathway of interest. iMPAQT provides high quantitative accuracy. It allows to detect small changes under various…

Epsilon-Q
Desktop

Epsilon-Q

Performs automatically multiple spectral library searching, class-specific…

Performs automatically multiple spectral library searching, class-specific false-discovery rate (FDR) control and result integration. Epsilon-Q demonstrates good performance in identifying and…

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…

T3PQ
Desktop

T3PQ Top 3 Protein Quantification

An implementation of the method for Liquid Chromatography tandem Mass…

An implementation of the method for Liquid Chromatography tandem Mass Spectrometry (LC-MSE) applications. T3PQ is applicable to data generated on Fourier Transform-Ion Cyclotron Resonance (FT-ICR)…

Peakjuggler
Desktop

Peakjuggler

Allows label-free quantification of peptides and proteins. Peakjuggler is a…

Allows label-free quantification of peptides and proteins. Peakjuggler is a node for the Proteome Discoverer package.

mres2x
Desktop

mres2x

Analyzes reads Mascot™ result files and extracts either selected or all…

Analyzes reads Mascot™ result files and extracts either selected or all information in order to store it in a single file or multiple files in formats which are easier to handle downstream of…

MS2 Spectrum…
Desktop

MS2 Spectrum Processor

Allows deisotoping of isotopic clusters and charge deconvolution. MS2 Spectrum…

Allows deisotoping of isotopic clusters and charge deconvolution. MS2 Spectrum Processor was built to be used with Thermo Scientific Proteome Discoverer.

QuiXtoQuiX
Desktop

QuiXtoQuiX

Analyzes protein quantifications derived from MS1-spectra. QuiXtoQuiX is an…

Analyzes protein quantifications derived from MS1-spectra. QuiXtoQuiX is an open source software, part of QuiXoT software package, which detect the MS1-spectra contained in a specific precursor ion…

InfernoRDN
Desktop

InfernoRDN

Performs various downstream data analysis, data reduction, and data comparison…

Performs various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation. InfernoRDN is an R package that…

ProteoIQ
Desktop

ProteoIQ

A comprehensive suite to validate and quantify proteins by combining results…

A comprehensive suite to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. With dynamic extracted ion chromatogram plots, the…

MS-Spectre
Desktop

MS-Spectre

A visualisation and analysis tool for mass spectrometry. MS-Spectre provides…

A visualisation and analysis tool for mass spectrometry. MS-Spectre provides analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. MS-Spectre incorporates…

MFPaQ
Desktop
Web

MFPaQ Mascot File Parsing and Quantification

A web application dedicated to parse, validate, and quantify proteomics data.…

A web application dedicated to parse, validate, and quantify proteomics data. MFPaQ allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic…

RIPPER
Desktop

RIPPER

A framework for mass-spectrometry-based label-free relative quantification for…

A framework for mass-spectrometry-based label-free relative quantification for proteomics and metabolomics studies. RIPPER combines a series of previously described algorithms for pre-processing,…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.