In silico analysis software tools | Mass spectrometry based untargeted glycomics
The successful interpretation of mass spectrometry data often depends on the comparison of the detected signals with theoretical features of a putative molecule: Isoelectric point, retention time, sequence digestion, decoy database generation, consider post-translational modifications, molecular formula prediction, FASTA sequence databases reader, isotopic distribution.
Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such as KNIME, Galaxy and WS-PGRADE, to facilitate bioinformatics research in the field of MS on all levels. The software provides pre-built and ready-to-use tools for analysis of both proteomics and non-targeted metabolomics data.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Manages proteomic mass spectrometry workflows and data analysis. Multiplierz provides a toolset of multiple methods for peptide identification, quantitation, reporting, as well as tools for easily manipulating standard data formats. This software is a Python library compatible with new reporting formats and high-level tools to achieve post-perform proteomic analyses. The architecture of the software environment has seamless integration with native data files via mzAPI.
Calculates the isotope distribution of peptide and nucleic acid species with complex labeling patterns. Isodist is a program that uses Fourier transform convolution. It also squares to fit the calculated distribution to a data set. It was developed to supports simultaneous calculation of isotope distributions for mixtures containing an arbitrary number of species. This method also automatically corrects for peak width, a machine-based mass offset and non-zero baseline.
Provides a memory-efficient calculation of isotope patterns. enviPat is an R package that provides instrument-specific envelope and centroid calculation, batch processing, and molecular formula parsing for a variety of adducts commonly formed during electrospray ionization (ESI). It was used to elucidate differences between relative and absolute pruning thresholds on the distortion of isotopic envelopes.
Computes isotopologues of chemical substances that can alternate between joint probability and peak height threshold. IsoSpec can: build subisotopotlogues, merge them into sets of isotopologues above a given threshold, and construct a sequence of consecutive thresholds. It generates optimal p-sets of isotopologues corresponding to threshold from sequence of thresholds and top probable subisotopotlogues.
Mass list file format conversions, protein sequence digestion, theoretical peptide and fragment mass computations, graphical display, matching with experimental data, isoelectric point estimation, peptide retention time prediction.
Provides a MS1 feature detection method. Dinosaur includes a plot trail and a strategy for performance monitoring, which was used to improve the algorithm in most major computational steps. It exposes more than 50 different configuration parameters, which are configurable directly on the command line or in a parameter file. This method can be incorporate in various workflows.
Performs comprehensive in silico analyses. LeTE-fusion gives an ideal estimation of peptide and variant peptide detections. It derives a realistic estimation of the percentage of detectable genome-annotated variants in shotgun mass spectrometry (MS) experiments using peptides with experimental evidence. This tool is useful for the assessment of feasibility of detecting other types of peptides or variations.
Provides features of interest for mass spectrometry. ChemCalc is a web application which allows to calculate molecular formula, molecular mass/molecular weight, exact mass (monoisotopic mass), elemental analysis and plots the isotopic distribution graph, find molecular formula from an accurate mass and also calculate peptide fragmentation. The application is available both through a user-friendly web interface and a developer-friendly Ajax programming interface.
Permits to calculate chemical formula and molecular weight of peptoids. Peptoid Calculator supports sequences up to 150 residues in length containing any combination of amino acids or peptoid building blocks present in the database related to the tool. It allows parentheses to be used to indicate repeat sequences within the input string. The tool can be useful for synthesize and/or use peptoids as part of a research in the biophysical and life sciences fields.
Calculates chemical formula and molecular weight of peptides. Peptide Calculator gives calculated values for isoelectric point (pI) and molar extinction coefficient as well as a plot of calculated b-strand propensity for a sequence. It provides a pie chart summarizing proportions of acidic, basic and uncharged residues in the sequence submitted. The tool is able to determine the molecular weights for all peptide/deletion/modification combinations incorporating single or double deletions and single or double modifications.
Allows users to determine theoretical isotopic distribution for molecules. MIDAs is an application available as both a software and a web interface. The program is made of two algorithms designed for identifying the targeted molecule in various formats for assessing coarse-grained isotopic distribution (CGIDs) and fine-grained isotopic distribution (FGIDs). Users can adjust the parameters by choosing an algorithm or by setting the distribution mass accuracy.
An efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, DeconTools is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.
Assists in the interactive calculation and visualization of isotope distributions. Envelope is an application capable of simultaneously calculating distributions for an arbitrary number of species of a single peptide or oligonucleotide. It can visualize experimental mass spectra, allowing the user to perform manual least-squares fits of calculated distributions to real experimental data. It can also be used as a teaching tool, and its interactive qualities make it well suited for use by research groups, in seminars, or in the classroom.
Allows quick generation of decoy databases for both separate and concatenated searches. DecoyPyrat is an efficient open source application that significantly reduces the inaccuracy in decoy databases. This method is adaptable and can be used with many user defined parameters such as digestion specificity. It also generates decoys in a hybrid reverse, switch and shuffle multi-step process.