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Metriculator

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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 understanding of metric values and an automated metric generation toolkit. The comparison plots are designed for at-a-glance determination of outliers and trends in the datasets, together with relevant statistical comparisons. Easy-to-use quantitative comparisons and a framework for integration plugins will encourage a culture of quality assurance within the proteomics community.

Pride Inspector

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 experimental output files, ranging from spectra and peptide and protein identification results to quantification data, using a modular and extensible set of open-source, cross-platform libraries. PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data.

Genoppi

Highlights biological relationships that might otherwise be difficult to discern. Genoppi integrates quantitative interaction proteomics data and results from genome-wide association studies (GWAS) or exome sequencing projects to proceed. It provides quality control (QC) of mass spectrometry-based interaction proteomics datasets and on-the-fly integrative analyses of the proteomic data and user-defined GWAS or exome sequencing studies. The tool can facilitate data sharing in cross-disciplinary collaborations.

iMonDB / Instrument MONitoring DataBase

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 parameters give a detailed account on the operation of a mass spectrometer, which can subsequently give insight into the observations in the mass spectral data. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. The iMonDB enables the monitoring of instrument parameters over a considerable time period, which fosters an additional approach to mass spectrometry quality control.

qcML

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 Initiative). This project develops and implements a data exchange format geared towards capturing quality control (QC) data from high-throughput biology experiments. The current focus of the project is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and next-generation sequencing as well.

MS-REDUCE

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 making it highly scalable with increasing number of spectra. MS-REDUCE is capable of eliminating noisy peaks as well as peaks that do not contribute to peptide deduction before any peptide deduction is attempted. Our experiments have shown up to 100× speed up over existing state of the art noise elimination algorithms while maintaining comparable high quality matches. Using our approach we were able to process a million spectra in just under an hour on a moderate server.

jqcML

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 work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA).

MSstatsQC

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 an open-source R package and Shiny web application for statistical analysis and monitoring of quality control and system suitability testing (SST) samples produced by spectrometry-based proteomic experiments. This package can be installed on a local server, and used via its web interface or via a command line.

KYSS / Know Your Samples

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 peptide identifications. KYSS facilitates the evaluation of sample preparation protocols, LC peptide separation, and MS and MS/MS performance by monitoring the number of missed cleavages, precursor ion charge states, number of protein identifications and peptide mass error in experiments.

AutoChrom

New
Associates instrument control for liquid chromatography (LM) with software for logical method development guided by quality by design (QdB) principles. AutoChrom offers as features data (1) interpretation with processing peak detection on single chromatograms and study of robustness, (2) method selection and optimization via several criteria and creation of method sequences, (3) project management with a dash board overview, and (4) the possibility of building a database with proper methods.

seamass-viz

Obsolete
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 LC-MS signal is decomposed into weighted B-spline basis functions that each represent a non-negative baseline component, peak, or peak shoulder. These building blocks are sorted and stored using an R-tree data structure that enables optimised retrieval both spatially and by their overall contribution to the signal. seamass-viz enables the mass spectrometrist to quickly inspect whole runs for ionisation/chromatographic issues, MS/MS precursors for coverage problems, or putative biomarkers for interferences, for example.