Data simulation software tools | Mass spectrometry-based untargeted proteomics
The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An alternative for creating gold standard data is to simulate it with features closely mimicking real data.
A fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility.
A collection of C++ programs for simulating ground truth LC-MS data and the subsequent application of custom data-dependent acquisition (DDA) algorithms. MSAcquisitionSimulator consists of three standalone command line programs. The first, FASTASampler, assists users in creating a FASTA file containing the proteins to be included in the simulation. Next, GroundTruthSimulator uses the previously created FASTA file and a configuration file containing simulation parameters to simulate digestion, residue modifications, retention time, chromatographic elution profiles, ionization efficiency, and charge and isotope distributions. Finally, the AcquisitionSimulator program takes as input the previously generated ground truth file and another configuration file. This program simulates a user-defined data-dependent acquisition algorithm on the ground truth data. It models ion accumulation, precursor scan spectra, scan time durations, and database search PSMs. MSAcquisitionSimulator provides an opportunity for researchers to test, refine, and evaluate novel DDA algorithms prior to implementation on a mass spectrometer.
Simulates and optimizes higher-energy collisional dissociation (HCD) phosphopeptide spectra. SimPhospho combines with spectral library by using SpectraST or through Trans-Proteomic Pipeline to search high accuracy and confident phosphosite validation. It provides a graphical user interface with a command line option and the possibility to choose a subset of input spectra or peptides for simulation.
Determines gradient retention times. HPLC Retention Predictor allows accurate retention prediction with virtually any gradient program, flow rate, column dimensions, and with any make/model of HPLC instrument. It is able to estimate the retention time of any compound in the retention database. This tool works by back-calculating the gradient profile and flow rate actually produced by a user's instrument.
Allows users to predict mass spectrum. MASSIS is an application which is built around four pivot databases gathering: functional group, cleavage rule, fragment intensity and small fragments, which are used to reproduce the mass spectra. This program performs its analysis through five main steps: (i) structure acquisition; (ii) identification of features; (iii) picking of the cleavage rules; (iv) deducing fragments/peaks intensities relationships and lastly (v) mass spectra rebuilding.
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