MS related tools

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Oligonucleotides

Mongo Oligo Mass Calculator v2.08

This program returns, from a given sequence of nucleic acids, the theoretical monoisotopic and average masses with different adducts, the list of CID fragments including base loss (a-B, w, y and d-H₂O) and internal fragments, and products of digestion by specific enzymes. In addition, a list of known RNA modifications database is available with a user defined nucleic acid for any other modification

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Oligo II

on-line calculator, written in JavaScript and should run on any browser having the JavaScript option enabled. Oligonucleotide mass calculator, uses compositions as input.

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Oligo Composition Calculator

on-line calculator, written in JavaScript and should run on any browser having the JavaScript option enabled. Finds nucleotide compositions from a given mass. User defined residues can be included..

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MolE

on-line calculator, written in JavaScript and should run on any browser having the JavaScript option enabled. Calculates molecular masses and isotope ratios from elemental compositions…

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SOS 1.0

SOS (Simple Oligonucleotide Sequencer) is an interactive tool for manual sequencing of oligonucleotides. It has a graphical interface and allows to determine oligonucleotide sequences from CID MS/MS data. It ses mass/intensity lists as input. Allows to check for the presence of modified residues. Available upon request here. See: JASMS 2002, 13, 200-203.

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OMA & OPA

The tool can rapidly calculate all theoretically possible fragment ions for a given input sequence and annotate them to an experimental spectrum, thus, saving a large amount of manual processing time. The OMA & OPA software is programmed in the platform-independent language Java and it therefore runs on all major operating systems.

Go to OMA &OPA

RoboOligo

An interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity coring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. Available upon request

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RAMM v2.0

Allows interpretation of collisional-induced dissociation (CID) data from oligonucleotides. RAMM can map interpreted tandem mass spectrometry (MS/MS) sequences onto RNA sequences. It enables higher throughput RNA modification mapping by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS). This tool supports five different ribonucleases for in silico digestion: RNase T1, RNase U2, RNase A, RNase MC1 and Cusativin. Available upon request

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Peptides and Proteins

ProteinProspector v6.2.1

Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments

Go to ProteinProspector

ProSight Lite

ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations.

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ORIGAMI

A Software Suite for Activated Ion Mobility Mass Spectrometry Applied To Multimeric Protein Assemblies. ORIGAMI is a two component software suite for faster acquisition of actived ion mobility mass spectrometry (IM-MS) datasets and analysis of MS and IM-MS data

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CIU Suite

Provides a way of differentianting proteins of similar structure as well as measure the stability of proteins. CIU has been used for a variety of applications such as differentiating binding modes of different ligands, distinguishing isocross-sectional proteins,

Go to Ciu Suite

Proline

An open source data integration framework and a software suite for mass spectrometry based proteomics.

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TDvalidator

Software to advance your proteoform analysis by allowing robust proteoform interrogation. A matching routine enables customized fitting of ions to their theoretical counterparts. under request

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Polymers

msXpertSuite

Allows modelling, simulation and analysis of ionized flying species. msXpertSuite provides (1) massXpert with a sub-module for defining new polymer chemistries, a desktop calculator, polymer sequence editor and a chemical center, and a data mining center.

Go to msxpertsuite

Theoretical calculations

ElComp

on-line calculator, written in JavaScript and should run on any browser having the JavaScript option enabled. Calculates elemental compositions from a given molecular mass.

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Molarity calculator

on-line calculator for usual chemical operations

Go to Molarity Calculator

EnviPat

Molecular formula analysis. Calculation of isotopic distributions with different adducts

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Chemcalc

MF analysis & MF finder

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Ion Mobility

PULSAR

PULSAR is software for analysing ion-mobility mass spectrometry data. It handles importing mobility data, and organising spectra by experimental meta-information, and viewing mass and mobility spectra

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UniDec

Universal deconvolution of Mass and Ion Mobility spectra

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