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Isobaric labeling protein quantification software tools | MS-based untargeted proteomics

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter…
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…

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…

Multi-Q
Desktop

Multi-Q

A fully automated tool for multiplexed iTRAQ-based quantitation in protein…

A fully automated tool for multiplexed iTRAQ-based quantitation in protein profiling, which is designed as a generic platform that can accommodate various input data formats from search engines and…

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…

isobar
Desktop

isobar

Provides methods for preprocessing, normalization, and report generation for…

Provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data tagged with isobaric labels, such as iTRAQ and TMT. The…

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…

COMPASS
Desktop

COMPASS Coon OMSSA Proteomic Analysis Software Suite

Allows to realize the high-throughput analysis of proteomics data. COMPASS aims…

Allows to realize the high-throughput analysis of proteomics data. COMPASS aims to demonstrate and validate the basic peptide and protein identification workflow. It performs favourably in all…

Quant
Desktop

Quant

Demonstrates improvements in protein quantification using iTRAQ™. Precise…

Demonstrates improvements in protein quantification using iTRAQ™. Precise quantification data can be obtained at the protein level when using error propagation and adequate visualization. Quant…

IQuant
Desktop

IQuant

An automated pipeline for quantitative proteomics based upon isobaric tags.…

An automated pipeline for quantitative proteomics based upon isobaric tags. IQuant integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS…

IsobariQ
Desktop

IsobariQ

A program designed for use in quantitative mass spectrometry based proteomics.…

A program designed for use in quantitative mass spectrometry based proteomics. IsobariQ is a tool for accurate quantification of IPTL, iTRAQ and TMT data. It allows the user to examine proteomic data…

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…

ITMSQ
Desktop

ITMSQ Isobaric Tandem MS Quantification

A quantitative software tool to improve N- and C-terminal fragment ion pairs…

A quantitative software tool to improve N- and C-terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different…

jTraqX
Desktop

jTraqX

An easy-to-use tool for processing and visualizing protein quantification data.…

An easy-to-use tool for processing and visualizing protein quantification data. jTraqX is platform independent and is compatible with all available 4-plex isobaric tags. Moreover, it integrates with…

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…

Libra
Desktop

Libra

A module within the trans-proteomic pipeline to perform quantification on MS/MS…

A module within the trans-proteomic pipeline to perform quantification on MS/MS spectra that have isobaric multi-reagent labeled peptides. Libra can also be used on TMT labeled samples. There is no…

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