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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.
SSRCalc / Sequence Specific Retention Calculator
Calculates sequence-specific retention for the accurate peptide retention prediction in RP HPLC (Reverse Phase High-Performance Liquid Chromatography). SSRCalc was developed in conjunction with off-line HPLC-MALDI MS (mass spectrometry) and has collected a data set of ∼350 peptides. A flexible structure for the programming code allows easy adaptation to different chromatographic conditions. The tool has been extensively tested for a number of real samples, providing solid support for protein identification and characterization; correlations in the range of 0.95-0.97 R² value have normally been observed.
A simulation software for LC-MS and LC-MS/MS experiments. Starting from a list of proteins from a FASTA file, the simulation will perform in-silico digestion, retention time prediction, ionization filtering, and raw signal simulation (including MS/MS), while providing many options to change the properties of the resulting data like elution profile shape, resolution and sampling rate. Several protocols for SILAC, iTRAQ or MS(E) are available, in addition to the usual label-free approach, making MSSimulator the most comprehensive simulator for LC-MS and LC-MS/MS data.
GDG / Glycopeptide Decoy Generator
Enables determination of the accuracy of tools that assign glycopeptides to collision-induced dissociation (CID) data. GDG is a graphical method to generate glycopeptide decoys de novo. The software can also be easily incorporated into other bioinformatics tools designed to match glycopeptides to CID data. The decoys generated by GDG can be divided into three categories based on their glycan compositions: (i) decoys containing [HexNAc]2[Hex]1-n[Fuc]0-2, (ii) decoys containing [NeuNAc] and (iii) decoy glycopeptides not belonging to first categories.
2DE Tandem MS
A computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations—2D electrophoresis and tandem mass spectrometry both designed for use in studying the proteomes of single-celled organisms. 2DE Tandem MS uses several quantitative algorithms to guide its electrophoresis simulation. The display protein list’ feature allows the user to select specific proteins for removal from the gel before running the animations again. The search protein field feature allows the user to find specific proteins by either including or excluding search terms from the loaded proteins titles, functions, or sequences. 2DE Tandem MS employs several principles of biochemistry to illustrate the properties of gel electrophoresis and peptide fragmentation realistically.
Protein Digestion Simulator
Reads a text file containing protein or peptide sequences and outputs the data to a tab-delimited file. The Protein Digestion Simulator can optionally digest the input sequences using trypsin, partial trypsin rules, or various other enzymes. The digested peptides will also have predicted normalized elution time (NET) values computed for them. An advanced feature of the Protein Digestion Simulator is the ability to calculate the number of uniquely identifiable peptides within an input file using only mass, or both mass and NET, given user-defined tolerances.
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