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Mass spectrometry

Last Updated: 31-Jul-2014

Library resources for researchers using mass spectrometry.


New library materials on mass spectrometry

  1. Alisa G. Woods, Costel C. Darie, editors. 2014

  2. edited by Charles H. Wick. 2014

    Biology Library (Falconer) » Stacks » QP519.9 .M3 I346 2014

  3. Stephen Shrader. 2014

  4. John Greaves and John Roboz. 2014

  5. Mauro Sardela, editor. 2014


Selected textbooks

This book discusses the fundamentals of mass spectrometry. Since these basics (physics, chemistry, kinetics, and thermodynamics) were worked out in the 20th century, they are rarely addressed nowadays and young scientists have no opportunity to learn them. This book reviews a number of useful methods in mass spectrometry and explains not only the details of the methods but the theoretical underpinning.
Interpretation of Mass Spectra
4th ed. Mill Valley, Calif. : University Science Books, c1993.
Chemistry & ChemEng Library (Swain) » Stacks » QC454.M3 M39 1993
This book emphasizes the point that the most important part of learning how to interpret unknown mass spectra is to practice interpreting mass spectra. The book aims at correlating ion dissociation mecanisms on a much broader scale, with the emphasis on basic attributes such as ionization energies, proton affinities and bond dissociation energies. The authors also tried to show how these mechanisms are applicable to the unimolecular dissociations of ions formed by any ionization method, including the new methods for obtaining mass spectra of large molecules.
This text provides an easy-to-read guide to the concept of mass spectrometry and demonstrates its potential and limitations. Written by internationally recognised experts and utilising "real life" examples of analyses and applications, the book presents real cases of qualitative and quantitative applications of mass spectrometry.
This textbook covers the field of mass spectrometry across the chemical, physical, biological, medical and environmental sciences. Sufficient depth is provided for the reader to appreciate the reasons behind and basis for particular experiments. It is uniquely and logically organised to enable the book to form the basis for a university course in mass spectrometry at the undergraduate or postgraduate level.
This highly successful textbook, acclaimed for its comprehensiveness,  accuracy, and its many excellent illustrations and photographs now comes in its second edition.
Mass Spectrometry Basics
Boca Raton : CRC Press, c2003.
Medical Library (Lane) » Check Medical Library (Lane) catalog for status » (No call number)
Describes processes, applications, and the underlying science in a concise manner supported by figures and graphics to further comprehension. The text provides practical approaches to interpreting mass spectral data and step-by-step guides for identifying chemically relevant compounds. Also includes an extensive reference section and a quick guide to each chapter that offers immediate access to key information.
Mass Spectometry: Principles and Applications 3rd Edition
3rd ed. Chichester, West Sussex, England ; Hoboken, NJ : J. Wiley, c2007.
Chemistry & ChemEng Library (Swain) » Stacks » QD96 .M3 H6413 2007
The latest edition of a highly successful textbook, "Mass Spectrometry, Third Edition" provides students with a complete overview of the principles, theories and key applications of modern mass spectrometry. All instrumental aspects of mass spectrometry are clearly and concisely described: sources, analysers and detectors.


Databases with spectral peak searching

Wiley Registry of Mass Spectral Data online
Ninth Edition. [Hoboken, NJ ?] : John Wiley & Sons, [2010] ©2010.
This database contains three collections of MS data:  (1) Wiley Registry 9th – 670,000 classical EI spectra, 570,000 searchable structures  (2) NIST/EPA/NIH 2011 – 240,000 classical EI spectra, 210,000 searchable structures (3) Wiley MS – 100,000 classical EI spectra, 100,000 searchable structures   It is the largest mass spectral library that is commercially available. Coverage includes pharmaceuticals, illegal drugs, poisons, pesticides,steroids, natural products, chemical warfare agents,and environmental pollutants.   Search help: Getting Started (from Wiley) and SurfSpec Flash Movies (from UK's Chemical Database Service). (Structure searching)
SDBS includes 6 different types of spectra under a directory of the compounds. The six spectra are as follows, an electron impact Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), a 1H nuclear magnetic resonance (NMR) spectrum, a 13C NMR spectrum, a laser Raman spectrum, and an electron spin resonance (ESR) spectrum. It is possible to search by compound name, molecular formula, molecular weight, CAS Registry Number, number of atoms, and spectral peaks.
Web version 6.0. Boca Raton, FL : Chapman & Hall/CRC Press, c2002.
POC is a database that contains over 29,000 of the most commonly sought organic compounds, featuring physical data, spectral data, and structures. With a high quality display and powerful search capabilities, it acts as an easy-to-use tool for identifying unknown compounds or for locating additional data and references for a known compound. Search by spectral peak, molecular formula/elements, properties, and substructure. (Structure searching)

Databases with spectral diagrams or literature references

[Columbus, Ohio : American Chemical Society, Chemical Abstracts Service]
SciFinder is the most comprehensive database for coverage of chemistry & chemical engineering. It has the world's largest collection of organic and inorganic substance information. The web version of SciFinder provides integrated access to CAPlus, CAS Registry, CASREACT, CHEMLIST, and CHEMCATS which are produced by Chemical Abstracts Service, and to MEDLINE which is produced by the U.S. National Library of Medicine. Sources covered in SciFinder include 10,000 journals, patents from 63 patent authorities, book chapters, conference proceedings, dissertations, evaluated reference works, technical reports, as well as book reviews and biographical information. (Structure and Reaction Searching)
[Frankfurt, Germany ; New York, NY] : Elsevier
Available via the web, Reaxys Xcelerate contains an extensive repository of experimentally validated data that chemists need including structures, reactions (including multi-step reactions) and physical properties. Reaxys was formed by the merger of three databases: Beilstein Handbook of Organic Chemistry, Gmelin Handbook of Inorganic and Organometallic Chemistry, and the Chemistry Patent database. (Structure and Reaction Searching)
This searchable database provides authoritative, complete, and detailed listings of atomic weights and isotopic compositions of elements. The atomic weights are available for elements 1 through 118 and isotopic compositions or abundances are given when appropriate.
Web version. Boca Raton, FL : Chapman & Hall/CRC
Includes descriptive and numerical data on the chemical, physical and biological properties of compounds; systematic and common names of compounds; literature references; structure diagrams and their associated connection tables. CCD online includes: organic compounds (269,000 records); natural products (178,000 records); inorganic and organometallic compounds (103,000 records); drugs (44,000 records); and analytical reagents (14,000 records). (Structure searching)
[Washington, D.C.] : National Institute of Standards and Technology, [1998]
The NIST Chemistry WebBook contains: Thermochemical data for over 7000 organic and small inorganic compounds; thermochemistry data for over 8000 reactions; IR spectra for over 16,000 compounds; mass spectra for over 33,000 compounds; UV/Vis spectra for over 1600 compounds; electronic and vibrational spectra for over 5000 compounds; constants of diatomic molecules(spectroscopic data) for over 600 compounds; ion energetics data for over 16,000 compounds; thermophysical property data for 74 fluids.
Philadelphia, PA : Institute for Scientific Information, c1998-
Search over 12,000 core journals across the sciences, social sciences, and arts and humanities to find the high quality research. Move backward/forward in time using cited/citing reference identified by researchers. Updated weekly, includes Science Citation Index Expanded (1899-present), Social Sciences Citation Index (1898-present), Arts & Humanities Citation Index (1975-present), Conference Proceedings Citation Index- Science (1990-present), Conference Proceedings Citation Index- Social Science & Humanities (1990-present), Book Citation Index (2005-present), Index Chemicus (1993-present), and Current Chemical Reactions (1985-present; also includes Institut National de la Propriete Industrielle structure data back to 1840)). (Structure searching)
Santa Fe, N.M.: Deep Web Technologies
xSearch enables Stanford students and researchers to search multiple resources at one time.  The 250+ resources in xSearch include abstracts and indexes, full-text ejournal and ebook sites, patents, technical reports, reference materials, plus more.


Dictionary of Mass Spectrometry
Chichester, West Sussex, U.K. : John Wiley & Sons, 2009.
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD96 .M3 M3336 2009
This Dictionary is a starting point for all those new to the topic, as well as a useful reference on terminology for those already in the field. Fully illustrated in full colour, the Dictionary will aid scientists from all disciplines in becoming conversant in the language and terminology of mass spectrometry.
IUPAC compendium of chemical terminology
Version 1.0.0. [Research Triangle Park, N.C.] : International Union of Pure and Applied Chemistry, 2006.
Chemistry & ChemEng Library (Swain) » Media » QD5 .I86 2006
The Compendium is popularly referred to as the "Gold Book", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC "Colour Books" on chemical nomenclature, terminology, symbols and units, and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.
Premium collection Oxford ; New York, N.Y.: Oxford University Press, c2002-
Oxford Reference Online brings together language and subject reference works from one of the world's biggest and most trusted reference publishers into a single cross-searchable resource. The Premium Collection offers a huge range of fully-indexed, extensively linked, up to date, and cross-searchable dictionary, language reference, and subject reference works published by Oxford University Press.


The Encyclopedia is the most comprehensive analytical chemistry reference available, covering all aspects from theory and instrumentation through to applications and techniques. The chemistry and techniques are described as performed in the laboratory, in the field, or by remote sensing. The level of detail is similar to that of a laboratory protocol and, together with the cited references, will support the analysis of complex inorganic, organic and biological structures by researchers.
Encyclopedia of Mass Spectrometry
1st ed. Oxford, UK ; Sn Diego, CA : Elsevier Science, 2003-
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » QD96 .M3 E53 2003 V.1
This multi-volume work is the first to provide unparalleled and comprehensive coverage of the full range of topics and techniques. It is suitable for new graduate students who are interested but not yet versed in the subject of mass spectrometry. Techniques, methods and applications of mass spectrometry are described in considerable detail; including limitations, current problems, and areas in which the method does not succeed well.
San Diego, CA : Academic Press, c2000.
SAL3 (off-campus storage) » Stacks » QD95 .E55 2000 V.1
Short articles, each covering one aspect of spectroscopy, provide the professional spectroscopist working in academia or industry with the essential facts and background on areas of spectroscopy peripheral to their own. References at the end of each article directs the reader to the level of detail required for professional purposes.
7th ed. Weinheim, Germany : Wiley-VCH ; New York : J. Wiley & Sons, 2009-
"This state-of-the-art reference work details the science and technology in all areas of industrial chemistry. Subject areas include: inorganic and organic chemicals, advanced materials, pharmaceuticals, polymers and plastics, metals and alloys, biotechnology and biotechnological products, food chemistry, process engineering and unit operations, analytical methods, environmental protection, etc."


Due to its enormous sensitivity and ease of use, mass spectrometry has grown into the analytical tool of choice in most industries and areas of research. This unique reference provides an extensive library of methods used in mass spectrometry, covering applications of mass spectrometry in fields as diverse as drug discovery, environmental science, forensic science, clinical analysis, polymers, oil composition, doping, cellular research, semiconductor, ceramics, metals and alloys, and homeland security. The book provides the reader with a protocol for the technique described (including sampling methods) and explains why to use a particular method and not others.
CS-MS Practical Users Guide
2nd. ed. / Hoboken, N.J. : Wiley-Interscience, c2008.
Updated and expanded, the classic guide to GC/MS helps chromatographers quickly learn to use this technique for analyzing and identifying compounds. After explaining the fundamentals, it discusses optimizing, tuning, using, and maintaining GC/MS equipment; explores advances in miniaturized and field-portable GC/MS systems and microfluidic components; and more. Complete with a CD-ROM, it covers applications in the environmental laboratory and in forensics, toxicology, and space science. This is the premier resource for professionals in those fields and for students.
A handbook of derivatives for mass spectrometry
Chichester : IM Publications, c2009.
Chemistry & ChemEng Library (Swain) » Stacks » QD96 .M3 Z35 2009
Chemical derivatisation of functional groups has proved popular since the beginning of organic mass spectrometry as a means to enhance the stability and volatility of the analytes as well as facilitating structure elucidation. This book provides comprehensive information on the wide range of derivatisation methods. Each chapter looks at a particular area of derivatisation and includes extensive references to the literature for further research where necessary.
Consolidates the information LC-MS bioanalytical scientists need to analyze small molecules and macromolecules.  This book thoroughly examines fundamentals of LC-MS bioanalysis in drug discovery, drug development, and therapeutic drug monitoring; the current understanding of regulations governing LC-MS bioanalysis; best practices and detailed technical instructions for LC-MS bioanalysis method development, validation, and stability assessment of analyte(s) of interest; and experimental guidelines and protocols for quantitative LC-MS bioanalysis of challenging molecules, including pro-drugs, acyl glucuronides, N-oxides, reactive compounds, and photosensitive and autooxidative compound. 
LC-MS Practical Users Guide
Hoboken, N.J. : John Wiley, c2005.
Chemistry & ChemEng Library (Swain) » Stacks » QD79 .C454 M363 2005
LC/MS: A Practical User's Guide provides LC/MS users with an easy-to-use, hands-on reference that focuses on the practical applications of LC/MS and introduces the equipment and techniques needed to use LC/MS successfully. Following a thorough explanation of the basic components and operation of the LC/MS system, the author presents empirical methods for optimizing the techniques, maintaining the instrumentation, and choosing the appropriate MS or LC/MS analyzer for any given problem.
Mass Spectral and GC Data
2nd, rev. and enl. ed. Weinheim ; New York : VCH, 1992-
Chemistry & ChemEng Library (Swain) » Reference (non-circulating) » RS189 .P425 1992 F PT.1


Protocols & methods

In its four volumes, this major reference work contains a complete treatment of the theory and methodology of sampling in all physical phases and the theory of sample preparation for all major extraction techniques. Fundamentals of sampling and sample preparation are reinforced through comprehensive sections dealing with Biological and Medical, Environmental and Forensic, and Food and Beverage applications.
Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press, 2006-
This interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods—a mix of cutting-edge and well-established techniques. All protocols are up-to-date and presented in a consistent, easy-to-follow format.
Hoboken, N.J. : John Wiley.
Current Protocols is the largest collection of authoritative and regularly-updated step-by-step research techniques and procedures available. With over 20 years of experience and over 11,500 protocols, as well as expert Editorial Boards and a qualified in-house scientific editorial staff, Current Protocols is the leading source of high-quality protocols for life scientists worldwide.
Springer Protocols is the largest subscription-based electronic database of reproducible laboratory protocols in the Life and Biomedical Sciences. Compiling protocols from Humana’s successful book series Methods in Molecular Biology, Methods in Molecular Medicine, Methods in Biotechnology, Methods in Pharmacology and Toxicology, and Neuromethods, as well as from a vast number of Laboratory Handbooks, such as The Biomethods Handbook, The Proteomics Handbook, and the Springer Laboratory Manuals.

Mass spectrometry > methods

  1. edited by Rune Matthiesen. 2013

    Biology Library (Falconer) » Stacks » QH506 .M45 V.1007

  2. edited by Jennifer J. Kohler, Steven M. Patrie. 2013

    Biology Library (Falconer) » Stacks » QH506 .M45 V.951

  3. edited by Norbert W. Lutz, Jonathan V. Sweedler, Ron A. Wevers. 2013

    Biology Library (Falconer) » Stacks » QP171 .M49 2013

  4. edited by Walter A. Korfmacher. 2012

  5. edited by Perry G. Wang, Weixuan He.. 2011

    Medical Library (Lane) » Check Medical Library (Lane) catalog for status » CRCNETBASE


We have a campus-wide site license for ACD Spectrus Software and ACD’s NMR Prediction Suite. The desktop software is only available in PC format. Users must go to Swain Library in person to receive license key.  Also see: Spectrus Processor NMR Flyer

Prediction Software on the Web

2.0. [Toronto, Canada] : ACD.
The online ACD/I-lab prediction engine may be used to predict physicochemical properties, NMR spectra and chemical shifts and ADME toxicities. It also assesses prediction reliability and includes searchable content databases.  Also see: iLab Flyer

Site-licensed by Swain Library

Swain Library has purchased campus-wide site licenses for several products. Access to all of these products is limited to current Stanford students, faculty, and staff.

Some software licensed by Swain Library is also accessible using a web browser and Citrix plugin via CDSERVER. For more information, please see instructions for off-campus access to resources.

Computer clusters

Swain Library has 13 dual-boot Mac/Windows computers. SUNet ID is required for use. The following software is available (only viewable from on-campus):