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Peptide assignment validation software tools | MS-based untargeted proteomics

In a typical proteomic analysis, the tandem mass spectra from a LC-MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide…
Percolator
Desktop

Percolator

An algorithm for improving the rate of confident peptide identifications from a…

An algorithm for improving the rate of confident peptide identifications from a collection of tandem mass spectra. Percolator uses a semi-supervised machine learning to discriminate correct from…

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…

PeptideProphet
Desktop

PeptideProphet

Automatically validates peptide assignments to MS/MS spectra made by database…

Automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

iProphet
Desktop

iProphet

Permits to calculate more accurate posterior probabilities and estimate false…

Permits to calculate more accurate posterior probabilities and estimate false discovery rate (FDR) at the level of unique peptide sequences. iProphet allows easy integration of multiple database…

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…

Peptide…
Web

Peptide Calculator

Calculates chemical formula and molecular weight of peptides. Peptide…

Calculates chemical formula and molecular weight of peptides. Peptide Calculator gives calculated values for isoelectric point (pI) and molar extinction coefficient as well as a plot of calculated…

Peptoid…
Web

Peptoid Calculator

Permits to calculate chemical formula and molecular weight of peptoids. Peptoid…

Permits to calculate chemical formula and molecular weight of peptoids. Peptoid Calculator supports sequences up to 150 residues in length containing any combination of amino acids or peptoid…

PepDistiller
Desktop

PepDistiller

Designed to validate the peptide identifications obtained from MASCOT search…

Designed to validate the peptide identifications obtained from MASCOT search results.

OMSSAPercolator
Desktop

OMSSAPercolator

A software tool which interfaces OMSSA with Percolator, a post search machine…

A software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.

CRanker
Desktop

CRanker

A post-database searching software tool for peptide identification. The goal of…

A post-database searching software tool for peptide identification. The goal of CRanker is to identify correct PSMs output from the database searching tool SEQUEST. Compared with PeptideProphet and…

IPPD
Desktop

IPPD Isotopic Peak Pattern Deconvolution

Provides functionality to extract isotopic peak patterns from raw mass spectra.…

Provides functionality to extract isotopic peak patterns from raw mass spectra. IPPD offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the…

De-Noise
Desktop

De-Noise

An algorithm to reduce the number of incorrect peptide matches and maximize the…

An algorithm to reduce the number of incorrect peptide matches and maximize the number of correct peptides at a fixed false discovery rate using a minimal number of scoring outputs from the SEQUEST…

pRatio
Desktop

pRatio

Identifies protein and calculates the probability of random peptide matching.

Identifies protein and calculates the probability of random peptide matching.

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