Quality assessment software tools | Mass spectrometry-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 data.
Offers access to over 180 tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. GenePattern is a genomic analysis platform that provides tools in the form of modules. Users can submit their data and choose suitable settings for performing complex analyses without detailed knowledge of the underlying programming language, algorithms and settings.
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 plug-in software components that use computer vision to analyze electrospray conditions, monitor the chromatographic device for stable backpressure, interact with a column oven to control pressure by temperature, and ensure that the mass spectrometer is still acquiring data.
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.
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 can read files from most mass spectrometry vendors via ProteoWizard. It can be incorporated into any workflow in which search engine generates pepXML or mzIdentML files.
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.
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.