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Mass Spectrometry

Mass Spectrometry


Mass spectrometry is an analytical technique to measure the mass-to-charge ratio of ions that can be used to identify unknown compounds, determine the isotopic composition of elements in a compound, and quantify the amount of a compound in a sample.

Technically, the measurement is carried out with mass spectrometers. In these devices, the molecules to be examined are converted into the gas phase in a vacuum (desorption) and then ionized with an electron beam, for example. The resulting ions are accelerated by an electric field and fed to an analyzer, which separates them according to their mass-to-charge ratio m/z.

The molecules are often fragmented during the process, which is particularly desirable in the case of the comparatively complex biopolymers, because the fragments are more easily converted into the gas phase and the mass spectrometric analysis is facilitated.

Mass spectrometry is an analytical technique that is widely used today. Application examples are the analysis and characterization of chemical substances, the biochemical investigation of biomolecules, identification of medically relevant substances in body fluids and tissues, forensic investigations, doping controls, environmental analysis, etc.

In addition, there are various mass spectrometric techniques and devices that differ depending on the technical design, application and accuracy. Since the resulting amount of data is quite small, mass spectrometers can easily be coupled to databases storing mass spectra. In addition, it is easy to couple a mass spectrometer to a gas chromatograph or HPLC system, allowing appropriate fractions of the sample to be analyzed.

Online available information resources on Mass Spectrometry: tutorials, lecture notes, databases, software, journals, institutions etc.

Content, Topics

General Information

Mass Spec Tips
... is a collection of tips relating to the operation and service of mass spectrometers. Scientific Instrument Services, SIS, USA

Mass Spectrometry
Tutorial: What is Mass Spectrometry?

Mass Spectrometry
Tutorial: Understanding Chemistry

MS Tools
An information source for the entire mass spectrometer community. Scientific Instrument Services, SIS, USA

TOF Mass Spectrometer
... is a instructional tutorial dealing with the fundamentals of Time of Flight (TOF) technology. It begins with a basic explanation of ion creation, separation and detection followed by a more advanced discussion of ion separation, the use of a reflector (RETOF), and second order focusing

Lecture Notes, Tutorials

Interpretation of mass spectra
Tutorial - Format: PDF

Mass Spectrometry
An introductory tutorial for students

Mass Spectrometry
Lecture notes

Mass Spectrometry and Chromatography
Lecture notes - Format: PDF

Special Information

Application Notes
Over 80 articles on Thermal Desorption, MS Direct Probe, and SIMION, including papers we presented at PittCon, ASMS, and EAS. Scientific Instrument Services, SIS, USA

Electrospray Ionization Mass Spectrometry
An introduction - Format: PDF

Electrospray Mass Spectra
Interpreting Electrospray Mass Spectra. IonSource.Com tutorial

Ionization Methods in Organic Mass Spectrometry
Analytical Instruments Documents. Jeol, USA

Miniature mass spectrometry
Links to miniature mass spectrometry and mobile GC/MS

Historical Facts and Documents

Data and Databases

Delta Mass
A Database of Protein Post Translational Modifications. ABRF, USA

Exact Masses and Isotopic Abundances
Alphabetic Listing of Elements. Scientific Instrument Services, SIS, USA

A powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases. Matrix Science

Mass Frontier
... provides you with the tools required to transform mass spectral data into results - fast!. Thermo

Mass Search
Searching SwissProt or EMBL by protein mass after digestion. ETH Zürich

Mass Spectrometry Data
Mass Spectrometry Data at Widener contains mass spectrometry data obtained at Widener University

NIST Standard Reference Database 1
NIST/EPA/NIH Mass Spectral Library (NIST 05) ASCII Version

NIST Standard Reference Database 1A
NIST/EPA/NIH Mass Spectral Library with Search Program

Spectral Databases
More resources ...

Wiley Registry of Mass Spectral Data
... is one of the most trusted and comprehensive mass spectral libraries in the world, and the gold standard for detection, identification and quantification in forensics, the environment, toxicology, and homeland security

Software and Tools

Elemental Composition Calculator
Online calculator. University of Utah, USA

Exact Mass Calculator, Single Isotope Version
... is a very primitive exact mass calculator. Given the formula of a chemical species, the calculator determines the exact mass of a single isotope of that species and the relative abundance of that isotope. Scientific Instrument Services, SIS, USA

FDM - Reference Spectra Databases
Infrared, Mass, NIR and Raman spectra, and software

Formular Finder
From the input parent peak and fragment masses all possible formulas are generated and formulas for the parent peak that are inconsistent with the fragment formulas are dropped

Fragment Finder
... provides a list of possible formulas for a given fragment mass

Global Proteome Machine
Proteomics data analysis, reuse and validation for biological and biomedical research, GPM. Rockefeller University, USA

Isotope Cluster
... calculates the isotope pattern for a given molecular formula. It includes 3rd and 4th period representative and transition metal elements

Isotope Distribution Calculator and Mass Spec Plotter
The program can calculate the isotopic distribution of a given chemical species. It can also plot either calculated or manually inputted isotopic distributions. Scientific Instrument Services, SIS, USA

... as a JCAMP-DX Data Viewer for Windows

A Program Predicting Mass Spectra of Combinatorial Libraries

Mass Spectrum Generator
Mass Spec Tools. Scientific Instrument Services, SIS, USA

Theory and Windows-based program to calculate mass spectra. For research and for teaching mass spectrometry and reaction kinetics

Metal Complex Finder
... finds the formula for an inorganic complex

Molar Mass Finder
... provides a list of possible molecular ion molar masses from given fragment masses

Mongo Oligo Mass Calculator
The ultimate oligonucleotide mass calculator, calculates also electrospray series, CID fragments, endo- and exonuclease fragments. Includes the possibility for calculating modified residues. University of Utah, USA

MS Wizzard
Spectroscopic Tool. University of Potsdam

SIS offers some of the most popular titles of mass spec and scientific software. Scientific Instrument Services, SIS, USA

Oligo Composition Calculator
Finds nucleotide compositions from a given mass. User defined residues can be included. University of Utah, USA

Oligo II Mass Calculator
Oligonucleotide mass calculator, uses compositions as input. University of Utah, USA

Advanced Oligo Design and Analysis

... is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum. Rockefeller University, USA

Peptide Mass Finder
... calculates the masses of ions for a given peptide sequence

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

... is designed to be a robust, easy to use aide-de-camp in the correlation and interpretation of LC/MS and MS/MS spectra to a known protein sequence or sequences. Download: Demo, Lite-Version

Solvent Cluster Ion Finder
... finds the formula for solvent cluster ions for the background in electrospray ionization MS

Tripeptide Mass Finder
... searchs for di- or tripeptide ions that match a given mass

... is a community supported, comprehensive database of protein modifications for mass spectrometry applications. OLS


Applied Spectroscopy
... publishes full-length articles, notes, and spectroscopic techniques. SAS

European Journal of Mass Spectrometry
... is a peer review journal covering all areas of mass spectrometry. Whilst “European” in its publishing base, its distribution, editors and authors are truly international. Sage

International Journal of Mass Spectrometry
The journal invites papers in all fundamental aspects of mass spectrometry and ion processes, including instrumental developments and applications in biology, chemistry, geology and physics. Elsevier

Journal of Mass Spectrometry
... publishes papers on a broad range of topics of interest to scientists working in both fundamental and applied areas involving the study of gaseous ions. Wiley - Interscience

Journal of the American Society for Mass Spectrometry
... is devoted to the rapid publication of comprehensive original research papers covering all aspects of mass spectrometry. Elsevier

Mass Spec Source
A newsletter designed for the mass spec community. Scientific Instrument Services, SIS, USA

Mass Spectrometry Reviews
Well-written reviews in selected topics in the various sub-fields of mass spectrometry. Wiley - Interscience

Rapid Communications in Mass Spectrometry
... is a journal whose aim is the rapid publication of original research results and ideas on all aspects of the science of gas-phase ions; it covers all the associated scientific disciplines. Wiley - Interscience

Articles and Reports

NEMS/mass Spectrometry System
Caltech physicists create first nanoscale mass spectrometer

Device can instantly measure the mass of an individual molecule.

[Image credit: Akshay Naik and Selim Hanay]

Research facilities and departments

MIT BEH Division of Toxicology; Mass Spectrometry Lab

San Francisco
Mass Spectrometry Facility. University of California, San Francisco, USA


American Society for Mass Spectrometry

Association for Mass Spectrometry
... of the German Physical Society e. V., DPG - [d]

Australian and New Zealand Society for Mass Spectrometry

Belgian Society for Mass Spectrometry

Biological Mass Spectrometry Laboratory

British Mass Spectrometry Society

Canadian Society for Mass Spectrometry

Dutch Society for Mass Spectrometry

German Society for Mass Spectrometry
DGMS - [d, e]

International Mass Spectrometry Foundation
The purpose of the IMSF is to advance the science and practice of mass spectrometry worldwide by the promotion and dissemination of knowledge

International SIMS Society
... is a non-profit community of SIMS scientists, engineers, educators, researchers, companies, institutions. SIMS = Secondary Ion Mass Spectrometry

Irish Mass Spectrometry Society

Mass Spectrometry Database Committee
American Academy of Forensic Sciences, Toxicology Section

Mass Spectrometry Society of Japan

Norsk Selskap for Massespektrometri
NSMS - [no]

Polish Mass Spectrometry Society
PTSM. Polskie Towarzystwo Spektrometrii Mas

Sociedad Española de Espectrometría de Masas
SEEM - [es]

Société Française de Spectrométrie de Masse
SFSM, french society of mass spectrometry - [f]

South African Association for Mass Spectrometry

Spanish Society for Mass Spectrometry
S. E. E. M. -

Swedish Mass Spectrometry Society
SMSS is a national organisation with the goal to favour research, education and propagation of mass spectrometric techniques in a broad sense

Swiss Group for Mass Spectrometry


Last update: 05.11.2022

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