Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Quality control software tools | MS-based untargeted proteomics

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw…
BatMass
Desktop

BatMass

A software package which allows to perform quick quality control of raw LC/MS…

A software package which allows to perform quick quality control of raw LC/MS data through its fast visualization capabilities. BatMass also serves as a testbed for developers of LC/MS data…

Metriculator
Desktop

Metriculator

A software tool designed to facilitate long-term storage of extensive…

A software tool designed to facilitate long-term storage of extensive performance metrics. Metriculator features a web interface that generates interactive comparison plots for contextual…

Pride Inspector
Desktop

Pride Inspector

A Java desktop application to visualise and perform first quality assessment on…

A Java desktop application to visualise and perform first quality assessment on Mass Spectrometry data and Proteomics. PRIDE Inspector supports the handling and visualization of different…

Genoppi
Desktop

Genoppi

Highlights biological relationships that might otherwise be difficult to…

Highlights biological relationships that might otherwise be difficult to discern. Genoppi integrates quantitative interaction proteomics data and results from genome-wide association studies (GWAS)…

iMonDB
Desktop

iMonDB Instrument MONitoring DataBase

Consists of a highly efficient database structure and associated software tools…

Consists of a highly efficient database structure and associated software tools to automatically extract, store, and manage mass spectrometry instrument parameters from raw data files. Instrument…

qcML
Format

qcML

An XML format for quality-related data of mass spectrometry that follows the…

An XML format for quality-related data of mass spectrometry that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards…

MS-REDUCE
Desktop

MS-REDUCE

An algorithm for ultrafast reduction of MS/MS data in pre-processing stage. The…

An algorithm for ultrafast reduction of MS/MS data in pre-processing stage. The proposed algorithm is a low-complexity procedure based on random sampling, approximate classification and quantization…

jqcML
Desktop

jqcML

A Java application programming interface (API) for the qcML data format. First,…

A Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and…

BACI-Q
Desktop

BACI-Q Bayesian Approach to Confidence Intervals for protein Quantitation

Supplies a software for depicting uncertainty in multiplexed proteomics. BACI-Q…

Supplies a software for depicting uncertainty in multiplexed proteomics. BACI-Q provides a statistical method, based on a hierarchical Bayesian model of a multiple condition Dirichlet-Multinomial…

MALDIrppa
Desktop

MALDIrppa

Allows user to control quality and analyze mass spectrometry (MS) data.…

Allows user to control quality and analyze mass spectrometry (MS) data. MALDIrppa simplifies detection of low-quality mass spectra and atypical peak profiles such as monitoring and data handling…

MSstatsQC
Web
Desktop

MSstatsQC

Uses statistical process control (SPC) tools to track metrics including total…

Uses statistical process control (SPC) tools to track metrics including total peak area, retention time, full width at half maximum (FWHM) and peak asymmetry for proteomic experiments. MSstatsQC is…

QuaMeter
Desktop

QuaMeter

An open-source tool that computes metrics to enable the QA/QC evaluation of…

An open-source tool that computes metrics to enable the QA/QC evaluation of proteomics instrumentation. It is a re-implementation of the NIST MSQC software with several important additions. QuaMeter…

SIMPATIQCO
Web

SIMPATIQCO SIMPle AuTomatIc Quality Control

A software package designed for evaluation of data from LTQ Orbitrap,…

A software package designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The…

SprayQc
Desktop

SprayQc

A real-time surveillance system that continuously monitors the status of the…

A real-time surveillance system that continuously monitors the status of the peripheral equipment to ensure that operational parameters are within an acceptable range. SprayQc is composed of multiple…

KYSS
Desktop
Web

KYSS Know Your Samples

A web application for analysis of large-scale proteomics datasets obtained by…

A web application for analysis of large-scale proteomics datasets obtained by liquid chromatography (LC) tandem mass spectrometry (MS/MS) analysis followed by database searching for protein and…

MS/MS Spectrum…
Web

MS/MS Spectrum Visualizer

A tool that visualizes a MS/MS spectrum and automatically highlights the b and…

A tool that visualizes a MS/MS spectrum and automatically highlights the b and y-ions. The highlighting is accomplished by taking an amino acid sequence you supply. The software then creates a…

seamass-viz
Desktop

seamass-viz

Interactively explores raw profile-mode quantitative LC-MS data with a 2D…

Interactively explores raw profile-mode quantitative LC-MS data with a 2D visualisation similar to Google Maps, but with an asymmetric encoding/decoding scheme specialised to the needs of MS. The…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.