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De novo peptide sequencing software tools | MS-based untargeted proteomics

De novo peptide sequencing by tandem mass (MS/MS) spectrometry is a valuable alternative to MS/MS database search. In contrast to the database search approach that utilizes the information from proteome, the de novo sequencing approach attempts to…
PepNovo
Desktop
Web

PepNovo

Provides high throughput de novo peptide sequencing analysis for tandem mass…

Provides high throughput de novo peptide sequencing analysis for tandem mass spectrometry (MS/MS) data. PepNovo modelizes peptide fragmentation events by using a probabilistic network. The software…

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…

DiagnoProt
Desktop

DiagnoProt

Clusters millions of spectra and uses machine learning to shortlist…

Clusters millions of spectra and uses machine learning to shortlist high-quality unidentified mass spectra that are discriminative of different biological conditions. DiagnoProt is able to shortlist…

Byonic
Desktop

Byonic

Provides sensitive and comprehensive peptide and protein identification from…

Provides sensitive and comprehensive peptide and protein identification from tandem mass spectrometry data.

pNovo+
Desktop

pNovo+

A de novo peptide sequencing algorithm using complementary HCD and ETD tandem…

A de novo peptide sequencing algorithm using complementary HCD and ETD tandem mass spectra.

Phenyx
Desktop

Phenyx

Software platform for the identification and characterization of proteins and…

Software platform for the identification and characterization of proteins and peptides from mass spectrometry data.

NovoHMM
Desktop

NovoHMM

A generative hidden Markov model (HMM) of mass spectra for de novo peptide…

A generative hidden Markov model (HMM) of mass spectra for de novo peptide sequencing.

Twister
Desktop

Twister

A software tool for de novo sequencing of proteins and peptides from tandem…

A software tool for de novo sequencing of proteins and peptides from tandem mass spectra. Given a set of deconvoluted top-down tandem mass spectra, Twister first generates a set of de novo sequences,…

MSNovo
Desktop

MSNovo

It works on data generated from both LCQ and LTQ mass spectrometers and…

It works on data generated from both LCQ and LTQ mass spectrometers and interprets singly, doubly, and triply charged ions.

UVnovo
Desktop

UVnovo

Applies a random forest algorithm to automatically learn from and then…

Applies a random forest algorithm to automatically learn from and then interpret ultraviolet photodissociation (UVPD) mass spectra, passing results to a hidden Markov model for de novo sequence…

MRUniNovo
Desktop

MRUniNovo

Parallelizes de novo peptide sequencing. Based on any Hadoop distributed…

Parallelizes de novo peptide sequencing. Based on any Hadoop distributed computing frameworks, MRUniNovo distributes different parts of a mass spectra dataset to different machines to be sequenced…

UniNovo
Desktop

UniNovo

A universal de novo peptide sequencing tool that works well for various types…

A universal de novo peptide sequencing tool that works well for various types of spectra and spectral pairs (e.g., CID, ETD, HCD, CID/ETD, etc).

Lutefisk
Desktop

Lutefisk

Allows de novo peptide sequence determinations from low-energy…

Allows de novo peptide sequence determinations from low-energy collision-induced dissociation (CID) data of tryptic peptides. Lutefisk is a program that rescores the final list of completed sequences…

NovoExD
Desktop

NovoExD

Provides a de novo peptide sequencing method for ExD spectra. NovoExD is a…

Provides a de novo peptide sequencing method for ExD spectra. NovoExD is a modified spectrum graph with multiple edge types, denoted as graph with multiple edge types (GMET), derived from to model…

Vonode
Desktop

Vonode

A de novo sequencing algorithm for shotgun proteomics using high-resolution…

A de novo sequencing algorithm for shotgun proteomics using high-resolution tandem mass spectrometry.

LysNDeNovo
Desktop

LysNDeNovo

Allows de novo sequencing of the Lys-N proteolytic peptides. LysNDeNovo is…

Allows de novo sequencing of the Lys-N proteolytic peptides. LysNDeNovo is based on simple and naive heuristics. It is able to confidently identify peptides without requiring any prior genome or…

SeqMS
Desktop

SeqMS

Aids to the sequencing of peptides by interpreting mass spectra. SeqMS is…

Aids to the sequencing of peptides by interpreting mass spectra. SeqMS is designed to aid in de novo sequencing, which is based on high-energy collision-induced dissociation (CID) tandem mass…

PepExplorer
Desktop

PepExplorer

Developed to use rigorous pattern recognition to assemble a list of homologue…

Developed to use rigorous pattern recognition to assemble a list of homologue proteins using de novo sequencing data coupled to sequence alignment to allow biological interpretation of the data.

NovoHCD
Desktop

NovoHCD

Combines amino acid combinations (AACs) and peptide tags to infer peptide…

Combines amino acid combinations (AACs) and peptide tags to infer peptide sequences. NovoHCD uses a modified spectrum graph model with multiple types of edges for peptide sequencing. This method uses…

TBNovo
Desktop

TBNovo

An algorithm for de novo protein sequencing by combining top-down and bottom-up…

An algorithm for de novo protein sequencing by combining top-down and bottom-up mass spectrometry. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass…

DeNovoGUI
Desktop

DeNovoGUI

A user-friendly and lightweight graphical user interface called DeNovoGUI for…

A user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use…

CycloBranch
Desktop

CycloBranch

A standalone, cross-platform and open-source de novo peptide identification…

A standalone, cross-platform and open-source de novo peptide identification engine for identification of nonribosomal peptides (NRPs) from MS/MS spectra. Currently, the identification of linear,…

Novor
Desktop

Novor

A real-time peptide de novo sequencing engine that achieved an…

A real-time peptide de novo sequencing engine that achieved an order-of-magnitude improvement on speed while maintaining the accuracy. Novor was designed to be a simple and flexible engine that can…

DirecTag
Desktop

DirecTag

An open-source algorithm to infer partial sequence tags directly from observed…

An open-source algorithm to infer partial sequence tags directly from observed fragment ions.

MetaSPS
Desktop

MetaSPS

Accurate de novo sequences from tandem mass spectrometry data at nearly full…

Accurate de novo sequences from tandem mass spectrometry data at nearly full sequence coverage.

Shotgun…
Web

Shotgun Protein Sequencing

Provides a method to interpret tandem mass (MS/MS) spectra which permitted de…

Provides a method to interpret tandem mass (MS/MS) spectra which permitted de novo sequencing of protein mixtures, including on ion trap instruments. Shotgun Proteins Sequencing allows users to…

AUDENS
Desktop

AUDENS

An open source tool for automated de novo peptide sequencing. AUDENS has a…

An open source tool for automated de novo peptide sequencing. AUDENS has a flexible preprocessing module which assigns relevances to putative b- or y-ions that are distinguished from all other peaks…

Antilope
Desktop

Antilope

Combines Lagrangian relaxation for solving an integer linear programming…

Combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen's k shortest paths algorithm.

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