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Database search software tools | MS-based untargeted proteomics

Protein identification and analysis by tandem mass spectrometry relies mostly on matching spectra to a database of protein sequences and scoring those matches.Source text:(Fournier et al., 2014) rTANDEM, an R/Bioconductor package for MS/MS protein…
MSPLIT-DIA
Desktop
Informed-Proteo…
Desktop

Informed-Proteomics

Allows top-down data analysis. Informed-Proteomics is composed of a liquid…

Allows top-down data analysis. Informed-Proteomics is composed of a liquid chromatography mass spectrometry (LC-MS) feature-finding algorithm, a database-search algorithm, and an interactive results…

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…

RAId-DbS
Web
Desktop

RAId-DbS

Assigns accurate spectrum-specific statistical significance to peptide hits.…

Assigns accurate spectrum-specific statistical significance to peptide hits. RAId_DbS is a peptide identification software that takes into account the integrated information of annotated single amino…

BiblioSpec
Desktop

BiblioSpec

Permits to create and search spectrum libraries. BiblioSpec is a flexible…

Permits to create and search spectrum libraries. BiblioSpec is a flexible spectrum comparison program that could be used in other applications such as for rapid detection of specific peptides of…

MS-GF+
Desktop

MS-GF+

Extends MS-GF to automatically derive scoring parameters from a set of…

Extends MS-GF to automatically derive scoring parameters from a set of annotated MS/MS spectra of any type. This database search tool based outperforms existing search engines in the analysis of ETD…

X! Tandem
Desktop

X! Tandem

Software that can match tandem mass spectra with peptide sequences, in a…

Software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.

Mascot Server
Web

Mascot Server

Allows users to identify, characterise and quantify proteins using mass…

Allows users to identify, characterise and quantify proteins using mass spectrometry (MS) data.

Andromeda
Desktop

Andromeda

Matches tandem mass spectrometry (MS/MS) spectra to peptide sequences in a…

Matches tandem mass spectrometry (MS/MS) spectra to peptide sequences in a database. Andromeda is a search engine based on a probability calculation for the scoring of peptide-spectrum matches. The…

SEQUEST
Desktop

SEQUEST

Correlates uninterpreted tandem mass spectra of peptides with amino acid…

Correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases.

rTANDEM
Desktop

rTANDEM

Interfaces the X!Tandem protein identification algorithm. rTANDEM can run the…

Interfaces the X!Tandem protein identification algorithm. rTANDEM can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters…

shinyTANDEM
Desktop

shinyTANDEM

This package provides a GUI interface for rTANDEM.

This package provides a GUI interface for rTANDEM.

PEAKS DB
Desktop

PEAKS DB

Identifies peptides from a sequence database with tandem mass spectrometry…

Identifies peptides from a sequence database with tandem mass spectrometry (MS/MS) data. PEAKS DB employs de novo sequencing as a subroutine and exploits the de novo sequencing results to improve…

MS-GFDB
Desktop

MS-GFDB

A database search tool based on MS-GF. MS-GFDB outperforms Mascot for ETD…

A database search tool based on MS-GF. MS-GFDB outperforms Mascot for ETD spectra or peptides digested with Lys-N. For example, in the case of ETD spectra, the number of tryptic and Lys-N peptides…

Gutentag
Desktop

Gutentag

An interactive, user-editable genetic sequence database tool, targeted at…

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups.

SpectraST
Desktop

SpectraST Spectra Search Tool

A spectral library building and searching tool designed primarily for shotgun…

A spectral library building and searching tool designed primarily for shotgun proteomics applications.

Comet
Desktop

Comet

Allows to research on mass spectrometry (MS)/MS sequence database. Comet…

Allows to research on mass spectrometry (MS)/MS sequence database. Comet identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. It is compatible with…

Param-Medic
Desktop

Param-Medic

Assesses experimental m/z error and derives parameters to search a Liquid…

Assesses experimental m/z error and derives parameters to search a Liquid Chromatography-Mass Spectrometry (LC−MS)/MS experiment. Param-Medic assumes that LC−MS/MS experiments are likely to make…

pFind
Desktop

pFind

Allows automated peptide and protein identification via tandem mass…

Allows automated peptide and protein identification via tandem mass spectrometry (MS/MS). pFind is a search engine that includes several algorithms, modules and workflows. An automatic estimation of…

Crux
Desktop

Crux

A database search program called Crux that reimplements and extends the widely…

A database search program called Crux that reimplements and extends the widely used database search program Sequest.

TopPIC
Desktop
SearchGUI
Desktop

SearchGUI

A user-friendly, lightweight and open-source graphical user interface for…

A user-friendly, lightweight and open-source graphical user interface for configuring and running the freely available OMSSA and X!Tandem search engines simultaneously.

MS2PIP
Desktop
Web

MS2PIP

An MS2 peak intensity prediction server that computes MS2 charge 2+ and 3+…

An MS2 peak intensity prediction server that computes MS2 charge 2+ and 3+ spectra from peptide sequences for the most common fragment ions. The server integrates the Unimod public domain…

ms1searchpy
Desktop

ms1searchpy

Identifies protein in complex mixtures. Ms1searchpy combines parallel digestion…

Identifies protein in complex mixtures. Ms1searchpy combines parallel digestion of the analyzed sample using different proteases, chemical reagents or their combinations, prediction of peptide…

MSPathFinder
Desktop

MSPathFinder

A database search engine for top-down proteomics. MSPathFinder is similar to…

A database search engine for top-down proteomics. MSPathFinder is similar to database search engines for bottom-up. It takes a fasta file, a spectrum file, and a list of modifications as an input and…

Cascaded search
Desktop

Cascaded search

An iterative procedure for incorporating information about peptide groups into…

An iterative procedure for incorporating information about peptide groups into the database search and confidence estimation procedure. cascade search provides a principled and flexible way to assign…

ProbIDtree
Desktop

ProbIDtree

Identifies automatically multiple precursors from single tandem mass…

Identifies automatically multiple precursors from single tandem mass spectrometry (MS/MS) acquisitions in high-throughput proteomics experiments. ProbIDtree is an algorithm that it (i) can identify…

MSBlender
Desktop

MSBlender

Improves identification of peptide-spectrum matches (PSMs) at low error rate.…

Improves identification of peptide-spectrum matches (PSMs) at low error rate. MSBlender is a unified probabilistic approach that delivers a method to estimate correct integrated error rates even…

Peptizer
Desktop

Peptizer

Aimes to separate true and false positive peptide identifications. Peptizer…

Aimes to separate true and false positive peptide identifications. Peptizer tests the peptide identifications by the evaluation of a series of user-selectable and extensible properties. The result of…

pTop
Desktop

pTop

A software tool to significantly improve the accuracy and efficiency of mass…

A software tool to significantly improve the accuracy and efficiency of mass spectral data analysis in top-down proteomics (TDP). The precursor mass offers crucial clues to infer the potential…

GlyDB
Dataset

GlyDB

Finds reliably glycopeptides from a few thousand collected tandem mass…

Finds reliably glycopeptides from a few thousand collected tandem mass spectrometry (MS/MS) spectra. The GlyDB approach was developed for annotation of low resolution spectra generated by ion trap…

CIDentify
Desktop

CIDentify Collision-Induced Dissociation identify

Helps to identify unknown peptides by mass spectrometry (MS). CIDentify is a…

Helps to identify unknown peptides by mass spectrometry (MS). CIDentify is a homology-based database search algorithm constructed from the source code for a FASTA homology-based database search…

DRIP
Desktop

DRIP Dynamic bayesian network for Rapid Identification of Peptides

A tool which utilizes a dynamic Bayesian network (DBN) for rapid identification…

A tool which utilizes a dynamic Bayesian network (DBN) for rapid identification of peptides in tandem mass spectra. Given an observed spectrum, DRIP scores a peptide by aligning the peptide's…

PIPI
Desktop

PIPI PTM-Invariant Peptide Identification

A method to achieve PTM-invariant peptide identification. PIPI first codes…

A method to achieve PTM-invariant peptide identification. PIPI first codes peptide sequences into Boolean vectors and converts experimental spectra into real-valued vectors. Then, it finds the top 10…

FDRAnalysis
Desktop

FDRAnalysis

Analyses the results from a number of different mass spectrometry (MS)/MS…

Analyses the results from a number of different mass spectrometry (MS)/MS search engines, based on decoy database searching. It accepts results in a number of different formats and outputs a list of…

Cycloquest
Desktop

Cycloquest

Identification of Cyclopeptides via Database Search of Their Mass Spectra…

Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases.

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…

MSFragger
Desktop

MSFragger

Represents a database search tool. MSFragger uses several large proteomic data…

Represents a database search tool. MSFragger uses several large proteomic data sets. It empowers the open database search concept for comprehensive identification of peptides and all their modified…

HiXCorr
Desktop

HiXCorr

A portable high-speed XCorr engine for high-resolution tandem mass spectrometry…

A portable high-speed XCorr engine for high-resolution tandem mass spectrometry by developing a novel algorithm for calculating XCorr. The algorithm enables XCorr calculation 1.25-49 times faster…

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…

LuciPHOr
Desktop

LuciPHOr

A site localization tool for generic post-translational modifications (PTMs)…

A site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data. LuciPHOr provides a site-level localization score for generic PTMs and associated…

IPeak
Desktop

IPeak

A peptide identification pipeline that is designed to combine the Percolator…

A peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without…

MsPI
Desktop

MsPI Mass spectrometry Protein Identification

Provides a complete procedure for protein identification by Peptide Mass…

Provides a complete procedure for protein identification by Peptide Mass Fingerprinting (PMF). MsPI is implemented as an exhaustive procedure that: (i) creates a reference database in which the…

Sipros
Desktop

Sipros

A database-searching algorithm for peptide and protein identification in…

A database-searching algorithm for peptide and protein identification in shotgun proteomics. Hybrid Message Passing Interface/OpenMP parallelism of the new Sipros architecture allowed its computation…

MS Amanda
Desktop

MS Amanda

A scoring system to identify peptides out of tandem mass spectrometry data…

A scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins. This algorithm is especially designed for high resolution and high accuracy tandem mass…

MetaMorpheus
Desktop

MetaMorpheus

Allows to search in proteomics database. MetaMorpheus integrates…

Allows to search in proteomics database. MetaMorpheus integrates post-translational modification (PTM) discovery capabilities. It analyses every database search result and for every frequently…

MassIVE
Dataset

MassIVE Mass spectrometry Interactive Virtual Environment

Promotes the global, free exchange of mass spectrometry data. MassIVE datasets…

Promotes the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange IDs to satisfy publication requirements. The dataset submission is only available to…

pCluster
Desktop

pCluster

A software tool for detecting protein modifications by tandem mass spectra…

A software tool for detecting protein modifications by tandem mass spectra clustering. pCluster contains two algorithms, one of which clusters spectra using precursor information and the other uses…

MS-Align+
Desktop

MS-Align+

A fast algorithm for top-down protein identification based on spectral…

A fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications.

MSPLIT
Desktop

MSPLIT

A spectral-library search tool for identification of mixture spectra of up to…

A spectral-library search tool for identification of mixture spectra of up to two peptides.

MixDB
Desktop

MixDB

A database search tool that is able to identify mixture MS/MS spectra from more…

A database search tool that is able to identify mixture MS/MS spectra from more than one peptide.

A A A
tsORFdb
Dataset

tsORFdb

Lists all possible sORFs (Small Open Reading Frames) from whole genome sequence…

Lists all possible sORFs (Small Open Reading Frames) from whole genome sequence data that can be predicted through bioinformatic approaches. tsORFdb is a web-enabled database that was developed for…

Morpheus…
Desktop

Morpheus search algorithm

A software tool designed specifically for high-mass accuracy data, based on a…

A software tool designed specifically for high-mass accuracy data, based on a simple score that is little more than the number of matching products. For a diverse collection of data sets from a…

X! HUNTER
Desktop
Web

X! HUNTER

Rather than predicting spectra from a peptide sequence, it directly compares an…

Rather than predicting spectra from a peptide sequence, it directly compares an input spectrum to a library of spectra that have been confidently assigned to a particular peptide sequence (an…

MyriMatch
Desktop

MyriMatch

A tool designed to take experimental data from shotgun proteomics experiments…

A tool designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins.

Pepitome
Desktop

Pepitome

A spectral library search engine which employs statistical systems for scoring…

A spectral library search engine which employs statistical systems for scoring spectrum-spectrum matches (SSMs).

Tremolo
Desktop

Tremolo

A spectral library search tool that leverages the Spectral Library Generating…

A spectral library search tool that leverages the Spectral Library Generating Function (SLGF) concept to identify spectrum-spectrum matches (SSMs).

MS Data Miner
Desktop

MS Data Miner

Aims at minimizing the time required for the analysis, validation, data…

Aims at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in mass spectrometry (MS) software. MS Data Miner was developed to…

BMF
Desktop

BMF Bitmapped Mass Fingerprinting

Provides a software for fast protein identification from protein databases.…

Provides a software for fast protein identification from protein databases. Bitmapped Mass Fingerprinting is a massively parallelized software that can leverage the power of supercomputers for fast…

amztpp
Desktop

amztpp

Allows the parallel execution of several different peptide identification…

Allows the parallel execution of several different peptide identification programs. amztpp is particularly useful on tandem mass spectrometry (MS/MS) data and can make analysis of large data sets.

ProbID
Desktop

ProbID

Identifies peptides from tandem mass spectra using a protein sequence database.…

Identifies peptides from tandem mass spectra using a protein sequence database. ProbID computes z-scores for the identifications and output the results in pepXML format, which subsequently can be…

MSGFPlus/MASIC…
Desktop

MSGFPlus/MASIC Data Processing Toolbox

Consists of a series of Windows batch files for the automated analysis of…

Consists of a series of Windows batch files for the automated analysis of Thermo .Raw files. MSGFPlus/MASIC Data Processing toolbox is an ensemble of software for running MSGF+ and MASIC. Following…

SimTandem
Desktop

SimTandem

A freely available tool for identification of peptides from LC-MS/MS spectra.…

A freely available tool for identification of peptides from LC-MS/MS spectra. SimTandem is based on a similarity search of mass spectra in a database of theoretical spectra generated from a database…

PeptideART
Desktop

PeptideART

A project to predict peptide fragmentation of mass spectrometry. PeptideART is…

A project to predict peptide fragmentation of mass spectrometry. PeptideART is a data-driven approach to learn peptide fragmentation rules in mass spectrometry, in the form of posterior…

MSPepSearch
Desktop

MSPepSearch

The program works by searching a peak list file against up to 4 MS/MS reference…

The program works by searching a peak list file against up to 4 MS/MS reference libraries.

PepFrag
Web

PepFrag

A tool for identifying proteins from a collection of sequences that matches a…

A tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.

pBuild
Desktop

pBuild

A tool that can compare several search engines' results and combine them…

A tool that can compare several search engines' results and combine them together.

OMSSA
Desktop

OMSSA Open mass spectrometry search algorithm

Provides a tandem mass spectra search engine. OMSSA is an efficient, sensitive,…

Provides a tandem mass spectra search engine. OMSSA is an efficient, sensitive, and specific algorithm for matching tandem mass spectrometry (MS/MS) peptide spectra. This resource is able to use…

MultiTag
Desktop

MultiTag

Assigns statistical significance to matches of multiple error-tolerant sequence…

Assigns statistical significance to matches of multiple error-tolerant sequence tags to a database entry and ranks alignments by their significance. The MultiTag approach has the distinct advantage…

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