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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.
Spectrum Clustering
Provides an implementation of clustering and merging methods for MS/MS data. Spectrum Clustering is a user-friendly software that supports various methods for spectrum similarity scoring, clustering, and merging. This application presents a graphical user interface to the user, which is divided into sections that correspond with the different tasks that can be performed: “input”, “similarity options”, “clustering options”, “merging options”, and “output”.
MSpC / Morpheus Spectral Counter
Calculates normalized spectral abundance factor (NSAF) values from output obtained from Morpheus, a peptide-mass spectrometry (MS)/MS matching engine compatible with high-resolution accurate-mass instruments. MspC calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. Morpheus/MSpC slightly outperformed TPP/ABACUS by having a greater overall accuracy, and by having more subunits showing an R2 linear correlation greater than 0.9.
MzJava
An open-source Java library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce and Apache Spark frameworks for cluster computing was implemented.
MS2Grouper
Provides a technique by which the false positive and false negative rates for similarity detection can be characterized. MS2Grouper is an algorithm that demonstrate the value of a paraclique-based criterion for assessing groups of similar spectra. The algorithm encompasses three main capabilities: (i) detecting similarity between spectra, (ii) assessing groups of related spectra on the basis of pairwise similarities and (iii) constructing a representative spectrum for each similarity group.
BioSunMS
Assists users in the management of patients information and serum peptide profiles-based statistical analysis. BioSunMS is a plug-in based and flexible software for mass spectrometry (MS) data management and analysis. It integrates patients data and MS data storage, process, sample classification and sample prediction into a single, user-friendly workbench. This system includes four functional modules: data management, spectrum processing, MS profile analysis and security module.
TurboRaw2MGF
There are a lot of high frequency, high abundance isobaric related ions in MS/MS spectrum, and combining removing isobaric related ions with deisotoping and deconvolution in MS/MS preprocessing procedure improves the peptide/protein identification sensitivity significantly. The user-friendly software package TurboRaw2MGF has been implemented for converting raw TIC data files to mascot generic format files and can be downloaded for free as part of the software suite ProteomicsTools.
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