Submission of Mass SpectraIntroductionMaSC invites members to contribute to its mass spectral database. This page describes file formatting requirements for data submission, and provides instructions for data conversion from various commercial data systems.MaSC JCAMP-DX Submission Instructions and TemplateInstructions (Adobe PDF format)Definitions and Notes on MaSC JCAMP Fields (Adobe PDF format) JCAMP Template (Excel format) JCAMP-DX and file submissionJCAMP-DX has been selected as the primary format for the database: this is a non-proprietary ASCII format developed by the Joint Committee on Atomic and Molecular Physical Data, and has the advantage that files can be imported and exported by a number of proprietary software programmes.In addition to compiling individual mass spectra in JCAMP-DX format, it is planned to create libraries of the spectra in NIST (National Institute of Standards and Technology) formats. This is intended to provide a means for organising and distributing data efficiently, and to facilitate computerised searching and matching with sample data by users. The compilation of data as both JCAMP-DX files and NIST formatted libraries will provide ready access to the raw spectral data, and allow convenient distribution and searching capabilities, to as many users as possible. While initial efforts are focussed on the compilation of mass spectra, the database will be expanded in the future to include other types of data including LC/PDA spectra and chromatographic data. There are two parts to a JCAMP-DX file: 1.) detailed header
information
about the sample itself, the instrumental conditions, the submitter,
and the data processing
Currently, the preferred method of submission is the MaSC Mass
Spectrum
Template (a MS Excel file). You will also need an ASCII text
editor
in preparing your mass spectral files for submission. Notepad or
Wordpad, which come standard with Microsoft Windows, will work but are
not recommended. If you don't have a good ASCII text editor, try Notetab Light, which
is freeware.2.) the mass spectral data in X, Y format. You will need to have previously saved the mass spectral data you wish to submit as an ASCII text file containing x,y values, where x corresponds to mass, and y corresponds to the intensity at that mass. There are instructions below for several commonly used data collection systems. We apologize if your system is not represented, and if you can supply a procedure for getting x,y data from your system's datafiles we will gladly include it here. General Notes on JCAMP-DX files:1. Basic structure:
3. Comments, which are ignored by data importers and translators, begin with $$ or ##=, and must finish at the end of the line on which they start. 4. Data records can be in any order with the exception of ##TITLE=, ##JCAMP-DX=, ##DATA TYPE=, and ##END= as described above. Mass Spectral Data Extraction Instructions
Useful Tools - MW Calculators and the likeChemIDPlus - CAS Number look-upMolecular Weight Calculation - Monoisotopic mass, nominal mass and average mass or something. MoIE - Molecular Mass Calculator at the University of Utah giving monoisotopic mass and average mass. Exact Masses and Isotope Abundance Ratios - A table of nominal masses in addition to exact masses, isotope ratios, etc. Kovats Index - MSView32 - This is useful for checking that you have created a proper J-CAMP file. WSearch32 - This is also useful for checking that you have created a proper J-CAMP file. Submission of Mass SpectraSubmit both the MS Excel file of the mass spectrum as well as its associated JCAMP-DX file to MaSC at spectra@mascgroup.orgPage last updated: September 5, 2006 |
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