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Isotopic labeling protein quantitation software tools | MS-based untargeted proteomics

With the advance of experimental technologies, different stable isotope labeling methods have been widely applied to quantitative proteomics.Source text:(Chang et al., 2014) SILVER: an efficient tool for stable isotope labeling LC-MS data…
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…

XPRESS
Desktop

XPRESS

A tool for quantifying ratios of differentially labeled proteins. XPRESS…

A tool for quantifying ratios of differentially labeled proteins. XPRESS calculates the relative abundance of proteins, such as those obtained from an ICAT-reagent labeled experiment, by…

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…

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…

PVIEW
Desktop

PVIEW

A computational analysis method that significantly improves the accuracy of…

A computational analysis method that significantly improves the accuracy of proteome-wide protein quantification from 15N mass spectra. PVIEW allows researchers in the fields such as microbiology to…

ASAPRatio
Desktop

ASAPRatio Automated Statistical Analysis on Protein Ratio

Calculates the relative abundances of proteins and the corresponding confidence…

Calculates the relative abundances of proteins and the corresponding confidence intervals from ICAT-type ESI-LC/MS data. ASAPRatio utilizes the signals recorded for the different isotopic forms of…

Isotopica
Web
Desktop

Isotopica

Supports calculation of the mass and theoretical isotopic distribution of a…

Supports calculation of the mass and theoretical isotopic distribution of a mixture of complex biopolymers. Isotopica is a useful application for validating an observed peak alongside the theoretical…

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…

RAAMS
Desktop

RAAMS Regression Analysis Applied to Mass Spectrometry

Interprets spectra of 18O-labeled peptides without requiring chemical…

Interprets spectra of 18O-labeled peptides without requiring chemical composition information derived from product ion spectra. RAAMS is able to measure the effective 18O incorporation rate due to…

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…

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…

IsoQuant
Desktop

IsoQuant

A SILAC-based proteomics quantitation software tool which is used to process…

A SILAC-based proteomics quantitation software tool which is used to process high mass accuracy mass spectrometry data. IsoQuant offers a convenient quantitation framework to calculate…

muxQuant
Desktop

muxQuant

A method for multiplexed quantitative proteomics using differential metabolic…

A method for multiplexed quantitative proteomics using differential metabolic stable isotope labeling and mass spectrometry. From accurate mass LC-MS data in mzXML aligned with peptide…

pepXML2Excel
Desktop

pepXML2Excel

An AWK program that transposes the peptide list in the TPP PepXML Viewer to one…

An AWK program that transposes the peptide list in the TPP PepXML Viewer to one protein per line, calculates averages, standard deviations, t-test and Bonferroni correction of the peptide ratios for…

LaCyTools
Desktop

LaCyTools

Tackles the individual aspects of a liquid chromatography-mass spectrometry…

Tackles the individual aspects of a liquid chromatography-mass spectrometry (LC-MS) experiment. LaCyTools deals with multiple charge states, giving an output per charge state if desired, and offers…

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…

ICPL_ESIQuant
Desktop

ICPL_ESIQuant

A proteomics software tool for quantitatively analyzing large mass…

A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. ICPL_ESIQuant is able to process mass spectrometric data…

EMU
Desktop

EMU Elementary metabolite units

Identifies minimum amount of information needed to simulate isotopic labeling…

Identifies minimum amount of information needed to simulate isotopic labeling within a reaction network. EMU is a bottom-up modeling approach based on a highly efficient decomposition algorithm. The…

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…

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…

SILVER
Desktop

SILVER

An efficient tool for quantification of the stable isotope labeling mass…

An efficient tool for quantification of the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein…

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