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Protein inference software tools | MS-based untargeted proteomics

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Due to the existence of degenerate peptides and 'one-hit wonders', it is very difficult to…
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…

PeptideClassifi…
Desktop

PeptideClassifier

Classifies shotgun proteomics data from any organism. PeptideClassifier carries…

Classifies shotgun proteomics data from any organism. PeptideClassifier carries out several steps: first, it analyzes protein sequence redundancies and generates an identifiable proteome index;…

ProteinProphet
Desktop

ProteinProphet

Automatically validates protein identifications made on the basis of peptides…

Automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

G T A T C G C T A
pepXMLTab
Desktop

pepXMLTab

Converts the “spectrum query” section of a pepXML file to a data frame and…

Converts the “spectrum query” section of a pepXML file to a data frame and filters the peptide spectrum matches (PSMs) based on a user-specified PSM false discovery rate (FDR) threshold.…

X-TandemPipelin…
Desktop

X-TandemPipeline

Allows the launching of database search engine, the interactive validation of…

Allows the launching of database search engine, the interactive validation of assignments and the automatic management of sequence redundancy for protein inference and phosphosite identification.…

TopMG
Desktop

TopMG

Identifies modified proteoforms using top-down tandem mass spectra, which is…

Identifies modified proteoforms using top-down tandem mass spectra, which is based on algorithms for the mass graph alignment problem. TopMG is a mass graph-based software tool for proteoform…

Mayu
Desktop

Mayu

Estimates false discovery rates (FDR) for protein identifications in large…

Estimates false discovery rates (FDR) for protein identifications in large scale data sets. Mayu is based on a target-decoy strategy. It can be applied to the results of any search and protein…

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…

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…

DeepPep
Desktop

DeepPep

Forecasts a set of protein from a standard proteomics mixture. DeepPep is a…

Forecasts a set of protein from a standard proteomics mixture. DeepPep is a deep learning-based framework allowing to work about deep protein inference. This tool enables quantification of the change…

PIA
Desktop
Web

PIA Protein Inference Algorithms

A flexible software suite for combining peptide spectrum matches (PSMs) from…

A flexible software suite for combining peptide spectrum matches (PSMs) from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data…

IsoformResolver
Desktop

IsoformResolver

Aims users to treat problems in protein inference for large data sets.…

Aims users to treat problems in protein inference for large data sets. IsoformResolver is a peptide-centric protein grouping methods allowing an analyze of results from many protein profiling…

RAId
Desktop

RAId

A protein ID method that combines peptide evidences of a candidate protein…

A protein ID method that combines peptide evidences of a candidate protein based on a rigorous formula derived earlier; in this formula the database P-value of every peptide is weighted, prior to the…

CEA
Web

CEA Clique Enrichment Analysis

A protein interaction network-assisted approach to improve protein…

A protein interaction network-assisted approach to improve protein identification in shotgun proteomics. The hypothesis of this method is that proteins eliminated as a result of insufficient…

ProLuCID
Desktop

ProLuCID

An algorithm for peptide identification using tandem mass spectrometry and…

An algorithm for peptide identification using tandem mass spectrometry and protein sequence databases. ProLuCID uses a three tier scoring scheme. First, a binomial probability is used as a…

PolyCut
Desktop

PolyCut

Assists mass spectrometry-based bioinorganic studies via top-down and bottom-up…

Assists mass spectrometry-based bioinorganic studies via top-down and bottom-up approaches in positive and negative ion modes. PolyCut is designed to cope with metalloproteins, metallo-polymers and…

plfdr
Desktop

plfdr

A decoy-free protein-level false discovery rate (FDR) estimation method. Our…

A decoy-free protein-level false discovery rate (FDR) estimation method. Our method consists of three key steps: (i) generating random bipartite graphs with the same structure; (ii) calculating the…

IDPicker
Desktop

IDPicker

An open-source protein assembly tool that derives a minimum protein list from…

An open-source protein assembly tool that derives a minimum protein list from peptide identifications filtered to a specified false discovery rate. By segregating peptide identifications for…

BagReg
Algorithm

BagReg

A learning-based method for protein inference. BagReg firstly artificially…

A learning-based method for protein inference. BagReg firstly artificially extracts five features from the input data, and then chooses each feature as the class feature to separately build models to…

decryptor
Web

decryptor

Analyses data from tandem mass spectrometry (MS) of human proteome for presence…

Analyses data from tandem mass spectrometry (MS) of human proteome for presence of point alterations. Subsequently, decryptor deduces DNA/mRNA alterations whenever possible. To use decryptor, users…

Barista
Desktop

Barista

A protein identification algorithm that combines two different…

A protein identification algorithm that combines two different tasks–peptide-spectrum match (PSM) verification and protein inference–into a single learning algorithm. Barista requires three…

OpenSea
Desktop

OpenSea

Matches de novo sequences to homologous proteins and overcomes many of the…

Matches de novo sequences to homologous proteins and overcomes many of the limitations of other sequence homology search algorithms. OpenSea was designed to align de novo sequences from all MS/MS…

MSBayesPro
Desktop

MSBayesPro

A Bayesian protein inference algorithm for LC-MS/MS proteomics experiment.…

A Bayesian protein inference algorithm for LC-MS/MS proteomics experiment. MSBayesPro is the proof-of-principle implementation of the Bayesian protein inference algorithm published in RECOMB 2008.

MSpresso
Desktop

MSpresso

A Bayesian score that estimates the posterior probability of a protein's…

A Bayesian score that estimates the posterior probability of a protein's presence in the sample given its identification in an MS/MS experiment and its mRNA concentration measured under similar…

ProteinLP
Desktop

ProteinLP

A linear programming model for protein inference. The main advantage of…

A linear programming model for protein inference. The main advantage of ProteinLP over other methods is the use of joint probability as the variable, which avoids modeling the protein probability and…

Fido
Desktop

Fido

A probabilistic model for protein identification in tandem mass spectrometry.…

A probabilistic model for protein identification in tandem mass spectrometry. Fido explicitly addresses the problems caused by “degenerate” peptides that occur in more than one protein.

DTASelect
Desktop

DTASelect

Assembles SEQUEST identifications and highlights the most significant matches.…

Assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed…

MassSieve
Desktop

MassSieve

A Java-based platform for visualization and parsimony analysis of single and…

A Java-based platform for visualization and parsimony analysis of single and comparative LC-MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment…

Scaffold
Desktop

Scaffold

A software tool designed to help scientists identify and analyze proteins in…

A software tool designed to help scientists identify and analyze proteins in biological samples. Using output files from MS/MS search engines, Scaffold validates, organizes, and interprets mass…

ProteinLasso
Desktop

ProteinLasso

Explores an ensemble learning strategy to address the sparsity parameter…

Explores an ensemble learning strategy to address the sparsity parameter selection problem in Lasso model. ProteinLasso has several advantages over the existing methods: (1) it casts the protein…

Spectrum Mill
Desktop

Spectrum Mill

Identifies proteins and peptides through fast database searches with automatic…

Identifies proteins and peptides through fast database searches with automatic or manual match validation and unique algorithms that minimize false positives. Spectrum Mill software can identify…

ProteinART
Web

ProteinART

A reformulation of the protein inference problem by utilizing the recently…

A reformulation of the protein inference problem by utilizing the recently introduced concept of peptide detectability. The current demo version handles no more than 100 proteins and 20 identified…

ProteinInfer
Desktop

ProteinInfer

Enables to obtain an analytical expression of protein inference. ProteinInfer…

Enables to obtain an analytical expression of protein inference. ProteinInfer proposes a combinatorial perspective of the protein inference problem. Use of combinatorial mathematics allows to…

PROVALT
Desktop

PROVALT

A heuristic method for organizing proteins identified at a specified…

A heuristic method for organizing proteins identified at a specified false-discovery rate using Mascot-matched peptides. PROVALT uses peptide matches from a random database to calculate…

EBP
Desktop

EBP Empirical Bayes Protein identification algorithm

A statistical method for estimating probabilities of protein expression that…

A statistical method for estimating probabilities of protein expression that integrates peptide sequence identifications from multiple search algorithms and replicate experimental runs. EBP is…

PANORAMICS
Desktop

PANORAMICS

A probability model for determining the likelihood that peptides are correctly…

A probability model for determining the likelihood that peptides are correctly assigned to proteins. This model derives consistent probability estimates for assembled proteins. The probability scores…

MSNet
Desktop

MSNet

Analyzes MS/MS experiments in the larger context of the biological processes…

Analyzes MS/MS experiments in the larger context of the biological processes active in a cell. MSNet improves protein identification in shotgun proteomics experiments by considering information on…

DBParser
Web

DBParser

Enhances the significance of data collected in large-scale shotgun tandem mass…

Enhances the significance of data collected in large-scale shotgun tandem mass spectrometry experiments using automated peptide sequence search engines. DBParser utilizes parsimony analysis to filter…

ComByne
Web

ComByne

A program for scoring and ranking higher-level identifications. Unlike other…

A program for scoring and ranking higher-level identifications. Unlike other identification integration tools, ComByne corrects for protein lengths; it also makes use of more information, such as…

Qscore
Desktop

Qscore

Measures the quality of the results for protein identifications obtained from…

Measures the quality of the results for protein identifications obtained from spectral matching of MS/MS data using the Sequest database search program. In direct comparison with a published method…

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