The Wayback Machine - https://web.archive.org/web/20110826012824/http://research.smilems.com/molecule-tk/
A molecule computational toolkit
This website is from the research team of
SmileMS software for MS2-based small molecule identification. Here you will find small utility tools that are useful for us in the context of our internal R&D.; We think that some of them might be useful so this website makes these tools available for the general community.
We are currently working on developments that incorporate the use and interpretation of MS1 data. The tools proposed here are simple utilities to calculate isotopic ratios and to propose atomic formulae and entries in PubChem based on exact mass information.
Play around with these tools and drop us an
email if you have questions, comments or suggestions.
If you want to know more about SmileMS software, see the
website and/or have a look at the
on-line viewer.
This version of SmileMS gives you the chance to explore the interface and view some examples of submissions and results.
Some functionalities are blocked so you cannot upload new analyses or libraries, for example.
A
full trial version is available for free download with a 21-day license.
Enjoy :)
A computational toolkit for MS data
The toolkit currently offers the following features
Calculator for low precision isotopic ratio distribution
For each atomic formula, the tool computes the corresponding theoretical isotopic masses and relative abundance. This is for low precision data, i.e. masses and abundances are averaged.
Calculator for high precision isotopic ratio distribution
For each molecule formula, the tool computes high precision isotopic masses and abundance, down to signals with intensity 0.1% of the highest.
Atomic formula generator (mass to formula finder)
Given one mass and a tolerance, a list of atoms and maximum occurrences for each of them, compute the list of atomic formulae that fulfills these conditions.
Mass based Pubchem (toxicology) content search tool
Given one mass and a tolerance, search into the toxicology subset of the NCBI Pubchem database all the molecules matching with the specified range. Pubchem CID are returned, with hyperlink to the corresponding database entries.
Restrictions and comments
-
To master the load on this public version, a time limit of 30 seconds is set for each query. To limit computation time, you can reduce the mass tolerance, the maximum occurrence of atoms, etc.
- Each tool takes lists of molecules as input and outputs result tables in multiple formats, i.e HTML, text, xml and json.
- We offer the possibility to consider molecules as protonated or not.
Release notes
Version 0.1 is out, check out the
release notes.
Participate
You found bugs? You have questions? You maybe even have suggestions?
Email the SmileMS R&D; team
Credits
This tool is based on the
Chemical Development Toolkit
