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.
A quantitative proteomics data processing approach that uses complementary fragment ions to identify multiple coisolated peptides in tandem mass spectra allowing for their quantification. This approach can be applied to any shotgun proteomics data set acquired with high mass accuracy for quantification at the MS1 level. The SuperQuant approach was developed and implemented as a processing node within the Thermo Proteome Discoverer 2.x.
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”.
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.
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.
Facilitates the visualization and exploration of spectra from open format mass spectrometry (MS) files. MathIOmica-MSViewer is an add-on graphical user interface (GUI) utility for the Mathematica software system. It has been designed for simplicity and quick access of spectra in large files, providing a GUI with search filtering capabilities. It is provided as a notebook that allows the user to open and view mzML and .mzXML spectra.
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.
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.
Provides a model of the electron-driven reactions occurring inside the mass spectrometer. ETDetective allows users to express the mass spectrum in terms of parameters such as the total intensity of reactions and the probabilities of the three studied reactions: Electron Transfer Dissociation (ETD), Proton Transfer Reaction (PTR), and Electron transfer with no Dissociation (ETnoD). ETDetective is designed as an extension to MassTodon workflow.
A combinatorial algorithm for spectral deconvolution. MS-Deconv (i) generates a large set of candidate envelopes, (ii) constructs an envelope graph encoding all envelopes and relationships between them, and (iii) finds a heaviest path in the envelope graph. MS-Deconv explicitly scores combinations of candidate envelopes rather than individual envelopes as in previous approaches.
Assists users to compare a collection of reference spectrum to other spectrum from one or more mzXml files. SpectrumFinder is a program that finds similarities between a tandem mass spectrometry (MS/MS) spectrum of reference and other MS/MS spectrums from the same instrument and the same biological sample. It searches similarities between MS/MS spectrums by using the "cosine similarity".
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.
Provides a GPU-based dimensionality reduction algorithm for tandem mass spectrometry (MS2) spectra. G-MSR is a program that can be used as a pre-processing step in reductive proteomics. It proposes two different structures: (i) binary spectra and; (ii) quantized indexed spectra (QIS) with the aim of optimizing the employment of GPU memory. It can be used for processing datasets which exceed the memory limits of a GPU.
Assigns and interprets the results of electron transfer driven reactions. MassTodon considers a set of known chemical reactions triggered by the electron transfer. This tool contains several functions, such as: (1) the preprocessing of the spectrum; (2) the generation of potentially observable chemical formulas; (3) the deconvolution of spectra; and (4) the pairing of fragment ions, resulting in estimates of the probabilities of the considered reactions and fragmentations.
A package for protein identification and quantification in biologic complex samples. It covers a wide range of possible proteomic analyses from proteins and peptides identification to post-translational modification. It searches in many databases (SEQUEST, Z-Core, Mascot, …) and several dissociation technics (CID, HCD, ETD) for complete analyses. Proteome Discover automatizes data analyse and allows to easily represent results thanks to modules like GO enrichment.
Scans a series of Mass Spectrometry (MS) data files. MS File Info Scanner extracts the acquisition start and end times, number of spectra, and the total size of the data. The software can generate overview plots for visual quality assessment of the data using the /Liquid Chromatography (LC) switch.
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