The Analytical Chemistry Springboard - Mass Spectrometry Links and Resources

The Analytical Chemistry Springboard

Mass Spectrometry Links and Resources

Base Peak
A comprehensive mass spectrometry web resource created and maintaied by Kermit K. Murray.
What is Mass Spectrometry?
This page briefly explains MS at the most basic level, and has a link that will take an interested cruiser further. Try this one if you're a newbie and came here "by mistake"!
Accelerator Mass Spectrometry
A powerful tool for detecting long-lived, cosmogenic isotopes, which provide chronometers for the study of human, and other biological events.
Accelerator Mass Spectrometry on the Internet
Links to accelerator MS on the Internet by Philipp Gartenmann at ETH Zürich.
American Society for Mass Spectrometry
ASMS was formed in 1969, for the purpose of promoting and disseminating knowledge of mass spectrometry and allied topics. Membership includes over 3,500 scientists involved in research and development. Members come from academic, industrial and governmental laboratories. Their interests include advancement of techniques and instrumentation in mass spectrometry, as well as fundamental research in chemistry, geology, biological sciences and physics.
Amino Acid Residue Masses
A table of residual masses for the common amino acids, with a link to a structural information database.
Australian and New Zealand Society for Mass Spectrometry
The ANZSMS brings together a broad spectrum of scientists who work with mass spectrometry. The aim of the Society is to promote mass spectrometry by providing contact with local and international leaders in all areas, and providing a forum, through its meetings, for the presentation of research in mass spectrometry and related disciplines.
British Mass Spectrometry Society
Its aims are to encourage participation in all aspects of mass spectrometry on the widest basis, to promote knowledge and advancement in the field and to provide a forum for the exchange of views and information.
CBRG ETHZ
The home page of The Computational Biochemistry Research Group of ETH Zürich provides a variety of search options into the SwissProt protein database: AllAll - Related peptide sequences (Trees, ancestral seq., MSA, predictions etc), AllAllDB - Querying the all-against-all database of SwissProt, MassSearch - Searching SwissProt or EMBL by protein mass after digestion, NuclPepSearch - Searching SwissProt for a nucleotide sequence, PepPepSearch - Searching SwissProt for a peptide sequence, TreeGen - Tree generation from distance data, PredictGenes - Predict and verify gene structure by alignment with homologous proteins, MultAlign - Multiple sequence alignment tools (recalculate, adjust, optimize, trees, score...), and MassDynSearch - Searches Swissprot with the masses of protein fragments after N- or C-terminal digestion.
Cheatham's Instrumentation Pages
Lists of WWW links of research groups and companies that use/manufacture Inductively Coupled Plasma Mass Spectrometry (ICP-MS), Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES), Thermal Ionization Mass Spectrometry (TIMS), and Stable Isotope Ratio Mass Spectrometry (SIRMS) instruments.
CIMAR Ion Cyclotron Resonance Program - NHFML
Overview of the ICR Program and Facilities
Delta Mass
A listing of average mass changes (in increasing order) caused by chemical modifications of peptides or proteins taking place in MS. The listing is ambitious, with links to many reactions and still a lot more pending. This table is mirrored in Germany.
Development of Particle Beam Interfaces for MS
Short description of the title project at Southern Illinois University at Carbondale.
Electron Binding Energies
A table compiled by Gwyn Williams, listing electron binding energies (in eV) for the elements in their natural forms. The energies are given relative to the vacuum level for rare gases and H, N, O, F, and Cl diatomic molecules; relative to the Fermi level for metals; and relative to the top of the valence band for semiconductors.
Electrospray Developments
Describes current development in electrospray ionization at DOE Ames Labs, Ames, IA, USA.
EMBL Mass Spectrometry Page
This link contains a list of MS resources on the web, and also some information local pages.
Evaluation of Desorption Mass Spectra
This EDMS-tool allows to search, view, convert and handle THD and CVO-coded spectra picked via the internet from any server abroad. The site requires a HTML 3.0 compatible browser such as Netscape 1.1 or later.
Exact Mass
The calculation of the exact mass of any given compound is simple, but you have to have the right tool for the job. The most important tool to have is a table of exact masses. Any given element has one or more naturally occuring isotopes. Most periodic tables list the mass of an element out to several decimal places, but this is the average mass for that compound, i.e., the average of the exact masses of all of the naturally occuring isotopes, weighted by their percent abundance. To obtain the exact mass of a given compound, one must use the exact masses of only the most abundant isotopes for each element present. The table at this link lists each element and the mass of its most abundant isotope to four decimal places.
Fast Fourier Transforms
Details of how the FFT works is not explained in this tutorial, as this would involve too much complex mathematics. Instead it looks at the results produced by FFT and the ways it can be applied.
Flame Ionization Mass Spectrometry (FIMS)
A project exploring the viability of a chemical flame as an atomic ion source for a quadrupole mass spectrometer.
Fragment Wizard
The MS-Fragment Wizard can help you to interpret your MS spectra.
Fragment-Ion Tag Searching at UCSF
A database searching tool from the UCSF Mass Spectrometry Facility that can be used to fit the fragment-ion tag data contained in a user's tandem mass spectrum to a peptide sequence in an existing database. A Fragment-Ion Tag may consist of 1 to ~10 fragment-ion masses. All fragment-ions in the tag need not be of the same ion series, and amino-acid composition from immonium ions can be added. The allow errors feature enables matching to database sequences which contain a single mutation, cross-species substitution, or modified amino acid.
Hints in Mass Spectrometry
A couple of tips on how to do MS/MS with a double focusing sector instrument with linked scan runs, and how to use daughter ions and neutral loss scans to sequence oligopeptides.
ICP-MS for Analysis of Microliter Samples and Solids
Inductively-Coupled Plasma-Mass Spectrometry is already a highly sensitive and selective method for elemental and isotopic analysis. This project will investigate the ability of a microscale nebulizer called a monodisperse dried microparticulate injector (MDMI), to improve the sensitivity, speed, accuracy, and precision of ICP-MS is determining stable elements and radionuclides.
Introduction to Mass Spectrometry
An MS tutorial from Science Hypermedia.
Ionization Methods Tutorial
Very short, but informative texts describing the various ionization modes in MS.
Italian Mass Spectrometry Home Page
An attempt to provide information regarding mass spectrometry and related topics.
Kevin Cowtan's book of Fourier
What is a Fourier Transform? This question is best answered with the aid of an example, which this page provides.
The LC/MS Home Page
This site provides a comprehensive listing of books, reviews, courses, meetings, manufacturers, and contract labs for any technique relating to LC/MS. The site is structured to assist the information gathering process for newcomers and problem solvers in LC/MS.
The Mass Spectrograph Home Page
Describes the mass spectrograph development at Indiana University and has a link to a mass spectrograph bibliography, in addition to a few links.
Mass Spectrometry Data at Widener
This page contains mass spectrometry data obtained at Widener University for an advanced spectroscopy course. Data were collected on a Finnigan 4000 quadrupole GC/MS using a Teknivent Vector/Two data acquisition system and illustrate the differences between electron (EI) and chemical (CI) ionization.
Mass Spectrometry to Speed DNA Detection
Researchers at the LBL Human Genome Center have constructed what they call a "time-of-flight mass spectrometry test stand" in which they will be testing different means of vaporizing and detecting molecules of DNA.
Membrane Inlet Mass Spectrometry Database
Database on Membrane Inlet Mass Spectrometry. Edited by Hans Degn and Frants Lauritsen, Physical Biochemistry Group, Odense University and Tapio Kotiaho, VTT, Espoo, Finland. You can add your data on MIMs Database.
MS-Digest
A protein digestion tool from the UCSF Mass Spectrometry Facility that extracts a protein from an existing database, performs an enzymatic digestion, and calculates the mass of each peptide. Specify the index number produced by MS-Fit or MS-Tag, or the database accession number.
MS-Fit
A peptide-mass fingerprinting tool from the UCSF Mass Spectrometry Facility that tries to fit a user's mass spectrometry data to a protein sequence in an existing database and thus predict the identity of the user's protein. The MS input data should be generated by analyzing the peptides produced by the enzymatic digestion of a user's protein.
MS-Fragment Ion
A tool from the UCSF Mass Spectrometry Facility that calculates the possible fragment ions resulting from fragmentation of a peptide in a mass spectrometer. Fragmentation possibilities for post-source decay (PSD), high-energy collision-induced dissociation (CID), and low-energy CID processes may be calculated. The fragment ion types seen in PSD are the default selections.
Multisite Research in Mass Spectrometry
A new program in graduate and post graduate education at the University of Delaware, The Johns Hopkins University, University of Maryland Baltimore County, and the DuPont Company. A special feature of the program involves industrial and academic laboratory rotations.
Mutation Mass Shifts
This table, listing delta masses between various amino acids, is intended to aid in explaining how an observed mass change could be explained as an amino acid mutation.
NYU/RU Shared Data Resource
A free, accessible World Wide Web resource for protein mass spectrometry and analysis, maintained by the mass spectrometry groups at Rockefeller and New York Universities. Contains links to MassBank - a protein mass spectrum database, Protein Identification - a database of protein cleavage products derived from known protein sequences, MatrixDepot - a collection of matrix compounds for MALDI, and several other tools.
On-line Energetic Ion Mass Spectrometer Data
One of the first energetic ion mass spectrometers to sample the ion plasma composition was flown on the ISEE-1 Satellite, one of thee satellites in NASA's International Sun-Earth Explorer (ISEE) program.
Particle-Solid Interactions Web Server
Contains information useful for researchers in the field of interactions of ions, electrons, and energetic photons with solids. Maintained by Raul Baragiola, University of Virginia.
PeptideSearch
PeptideSearch by EMBL Protein & Peptide Group is an advanced tool for protein database searching by mass spectrometric data, such as peptide mass maps or (partial) amino acid sequences. PeptideSearch is also available as a standalone Macintosh application which can be downloaded from the EMBL FTP-site.
ProteinProspector
This start page from UCSF Mass Spectrometry Facility containg the sequence database search tools MS-Fit (peptide-mass fingerprinting data from MS), MS-Tag (fragment-ion tag data from MS/MS), and MS-Edman (Edman microsequence/peptide MS data), as well as the Peptide/protein MS utility programs MS-Digest (peptide masses from enzymatic digestion of protein), MS-Product (fragment ion masses for peptide), and MS-Comp (AA compositions fitting parent mass and immonium ions). There's a European mirror site at Ludwig Institute for Cancer Research in London.
Pyrolysis mass spectrometry at Aberystwyth
Pyrolysis is the thermal degradation of complex material in an inert atmosphere or a vacuum. It causes molecules to cleave at their weakest points to produce smaller, volatile fragments called pyrolysate. A mass spectrometer can then be used to separate the components of the pyrolysate on the basis of their mass-to-charge ratio (m/z) to produce a pyrolysis mass spectrum, which can then be used as a "chemical profile" or fingerprint of the complex material analysed. The combined technique is then known as pyrolysis mass spectrometry (PyMS).
Recommended Values of the Fundamental Physical Constants
This document gives the values of the basic constants and conversion factors of physics and chemistry resulting from the 1986 least-squares adjustment of the fundamental physical constants as published by the CODATA Task Group on Fundamental Constants and as recommended for international use by CODATA.
Regular Expression Searching
A database searching tool from the UCSF Mass Spectrometry Facility that performs regular expression type searches on different fields in protein databases. If the search field is set to Amino acid sequence the program finds amino acid sequences in the selected database which match the regular expression entered.
Rockefeller University Laboratory for MS and Gaseous Ion Chemistry
Secondary Ion Mass Spectrometry
A short description of the SIMS technique.
Secondary Ion Mass Spectrometry WWW Server
Contains an International Directory of SIMS groups, links to SIMS Online, Discussions groups, Literature, etc. There's also an experimental frame version of this server.
SEQUEST
SEQUEST correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. SEQUEST will determine the amino acid sequence and thus the protein(s) and organism(s) that correspond to the mass spectrum being analyzed.
Software for Biological Mass Spectrometry
A listing of downloadable software, mostly originating from the EMBL.
Stable Isotope Mass Spectrometry Users Group
The Stable Isotope Mass Spectrometry Users Group held its first annual meeting at the University of East Anglia in January of this year. Over 120 delegates attended, with presentation of 35 talks and 20 posters. Following the success of the Inaugral Meeting, it has been decided that the Stable Isotope lab at UEA will maintain some pages which will cater specifically for the group.
University of Cambridge Mass Spectrometry Server
A well maintained department site. The theory link leads to a section on the theory of modern techniques of analyte ionization and mass analysis.
Yahoo - Spectroscopy
The science/chemistry/spectroscopy page of the Yahoo Index. You can submit your web page here.
European Mass Spectrometry
A peer reviewed journal covering all areas of mass spectrometry. Both abstracts and author information can be found at this link in HTML or Adobe Acrobat format.
Inorganic Mass Spectrometry
Found here are abstracts from Applied Spectroscopy Nov 1994, which has a special focus on inorganic mass spectrometry.
International Journal of Mass Spectrometry and Ion Processes
Tables of Contents service starting from January 1995.
Journal of the American Society for Mass Spectrometry
Tables of Contents service starting from January 1995.
Newsgroup sci.techniques.mass-spec
USENET newsgroup on mass spectrometry.

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Knut Irgum, Analytical Chemistry, Umeå University, S-901 87 Umeå, Sweden.