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PTM identification software tools| MS-based untargeted proteomics

Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins.Source text:(Kertesz-Farkas et al., 2014) PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the…
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…

SUMmOn
Desktop

SUMmOn

An automated pattern recognition tool that detects diagnostic PTM fragment ion…

An automated pattern recognition tool that detects diagnostic PTM fragment ion series within complex MS/MS spectra, to identify modified peptides and modification sites within these peptides. The…

Inspect
Desktop

Inspect

A MS/MS database search tool specifically designed to address two crucial needs…

A MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. InsPecT uses peptide…

PIQED
Desktop
ProteoModlR
Desktop

ProteoModlR

Permits quantitative mass spectrometry (MS) analysis of post-translationally…

Permits quantitative mass spectrometry (MS) analysis of post-translationally modified peptides and proteins for functional proteomics of cell signaling. ProteoModlR is intended for the analysis of…

pMatch
Desktop

pMatch

Identifies unanticipated post-translational modifications (PTMs) from tandem…

Identifies unanticipated post-translational modifications (PTMs) from tandem mass spectrometry (MS/MS) data. pMatch is a dedicated open spectral library search tool that supports an entire workflow…

ProSight Lite
Desktop

ProSight Lite

A free Windows application for matching a single candidate protein sequence and…

A free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Fixed or variable modifications, including both…

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…

PTMTreeSearch
Desktop

PTMTreeSearch

An algorithm that uses a large database of known PTMs to identify PTMs from…

An algorithm that uses a large database of known PTMs to identify PTMs from MS/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the…

DeltAMT
Desktop

DeltAMT Delta Accurate Mass and Time

A statistical algorithm for fast detection of abundant protein modifications…

A statistical algorithm for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. DeltAMT is based on the fact that the modified and…

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…

P-Mod
Desktop

P-Mod

Enables discovery and sequence mapping of modifications to target proteins…

Enables discovery and sequence mapping of modifications to target proteins known to be represented in the analysis or identified by Sequest. P-Mod matches MS/MS spectra to peptide sequences in a…

ISPTM
Desktop

ISPTM Iterative Search for identifying PTMs

A powerful tool for unbiased identification of many different PTMs with high…

A powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures. This approach consists of a basic search with no variable modification,…

QuickMod
Desktop

QuickMod

A spectral library search based MSMS data analysis tool, designed to identify…

A spectral library search based MSMS data analysis tool, designed to identify modified peptides. QuickMod performs favorably in terms of speed and identification rate when compared to other software…

PTM…
Desktop

PTM MarkerFinder

Screens the MS/MS spectra in the output of a database search (i.e., Mascot) for…

Screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, PTM MarkerFinder reports and annotates the HCD and the corresponding…

Identification…
Web

Identification of C-C bridges in ETD data

C-C (cysteine or disulfide bridges) can be identified using MS and ETD-MS/MS…

C-C (cysteine or disulfide bridges) can be identified using MS and ETD-MS/MS data, because of the instability of the crosslinks during the fragmentation process. Optionally, MS3 CID data of the…

MAUblSearch
Desktop

MAUblSearch

An improved workflow for identifying Ub/Ubl conjugation sites based on the…

An improved workflow for identifying Ub/Ubl conjugation sites based on the ChopNSpice and X!Tandem software. ChopNSpice is modified to generate Ub/Ubl conjugation peptides in the form of a…

ChopNSpice
Web

ChopNSpice

A free web application that can help with the identification of…

A free web application that can help with the identification of post-translational modifications (PTM) and modification sites by mass spectrometry. The application can easily interface with existing…

MODi
Web

MODi

Interprets tandem mass spectra of peptides with multiple post-translational…

Interprets tandem mass spectra of peptides with multiple post-translational modifications (PTMs). MODi is a convenient method that consists of five stages: peak selection, tag discovery, database…

VEMS
Desktop

VEMS Virtual Expert Mass Spectrometrist

Contains a range of versatile tools for data validation and mining. VEMS…

Contains a range of versatile tools for data validation and mining. VEMS performs linear recalibration of the fragments ions in a tandem Mass Spectrometry spectrum to theoretical fragment masses for…

ModifiComb
Desktop

ModifiComb

A fast and reliable method for mapping hundreds types of PTMs at a time,…

A fast and reliable method for mapping hundreds types of PTMs at a time, including novel and unexpected PTMs. The high mass accuracy of Fourier transform mass spectrometry provides in many cases…

PTMSearchPlus
Desktop

PTMSearchPlus

A software tool for the automated integration of accurate intact protein mass…

A software tool for the automated integration of accurate intact protein mass (AIPM) and bottom-up (BU) mass spectra searches/data in order to both confidently identify the intact proteins and to…

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