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Mass spectrometry

Last Updated: 10-Mar-2016

Library resources for researchers using mass spectrometry.


Handbook of Spectroscopy, 2nd Edition
Second, enlarged edition.
Stanford University Libraries » Online resource » eResource
"This second, thoroughly revised, updated and enlarged edition provides a straightforward introduction to spectroscopy, showing what it can do and how it does it, together with a clear, integrated and objective account of the wealth of information that may be derived from spectra. It also features new chapters on spectroscopy in nano-dimensions, nano-optics, and polymer analysis.  Clearly structured into sixteen sections, this Handbook covers everything from spectroscopy in nanodimensions to medicinal applications, spanning a wide range of the electromagnetic spectrum and the physical processes involved, from nuclear phenomena to molecular rotation processes.  In addition, data tables provide a comparison of different methods in a standardized form, allowing readers to save valuable time in the decision process by avoiding wrong turns, and also help in selecting the instrumentation and performing the experiments."


"Written by the founders of the SPARK program at Stanford University, this book is a practical guide designed for professors, students and clinicians at academic research institutions who are interested in learning more about the drug development process and how to help their discoveries become the novel drugs of the future. Often many potentially transformative basic science discoveries are not pursued because they are deemed "too early" to attract industry interest. There are simple, relatively cost-effective things that academic researchers can do to advance their findings to the point that they can be tested in the clinic or attract more industry interest."

Selected textbooks

Fundamentals of Mass Spectrometry
New York, NY : Springer, c2013.
Stanford University Libraries » Online resource » eResource
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.
Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th Edition
4th ed., repr. with corrections. Chichester, West Sussex, England ; Hoboken, NJ : John Wiley & Sons, [2008]
Stanford University Libraries » Online resource » eResource
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.
Mass Spectrometry: a Foundation Course
Cambridge : Royal Society of Chemistry, 2004.
Stanford University Libraries » Online resource » eResource
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.
Mass Spectrometry: A Textbook
2nd ed. Berlin ; London : Springer, 2010.
Stanford University Libraries » Online resource » eResource
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.
Stanford University Libraries » Online resource » eResource
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.
Measuring mass : from positive rays to proteins
Philadelphia : Chemical Heritage Press, c2002.
Chemistry & ChemEng Library (Swain) » Stacks » QD96 .M3 M43 2002
Measuring Mass: From Positive Rays to Proteins is part of a celebration of fifty years of the Annual Conference on Mass Spectrometry and Allied Topics. As such, it is intended not only for practitioners of mass spectrometry but also for the lay reader interested in knowing more about the field. Many who practice the art and science of mass spectrometry are unaware of how the technique is applied outside their particular area of expertise. This short exposition will provide the practitioner and lay reader alike with an appreciation for the diverse applications of mass spectrometry in present-day scientific endeavors. Measuring Mass is also intended to celebrate the major events in the history of mass spectrometry.


Databases with spectral peak searching

Wiley Registry of Mass Spectral Data online
Ninth Edition. [Hoboken, NJ ?] : John Wiley & Sons, [2010] ©2010.
Stanford University Libraries » Online resource » eResource
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)
Japan : AIST
Stanford University Libraries » Online resource » eResource
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.
Stanford University Libraries » Online resource » eResource
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)

Property Databases

Atomic weights and isotopic compositions with relative atomic masses - image cropped
[Gaithersburg, Md.] : NIST Physical Measurement Laboratory, 1999-
Stanford University Libraries » Online resource » eResource
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
Stanford University Libraries » Online resource » eResource
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]
Stanford University Libraries » Online resource » eResource
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.
[Frankfurt, Germany ; New York, NY] : Elsevier
Stanford University Libraries » Online resource » eResource
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)

Bibliographic Databases

[Columbus, Ohio : American Chemical Society, Chemical Abstracts Service]
Stanford University Libraries » Online resource » eResource
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)
[London] : Royal Society of Chemistry
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"Items in Analytical Abstracts fall into three main categories: Journal articles, technical reports, and books. More than 250 key international journals are scanned regularly by the Analytical Abstracts editorial team. Over 75% of the original material is published in English, with other major languages being French and German, Russian and other eastern European languages, Chinese, and Japanese." Updated monthly. Covers 1980-present.
Web of Knowledge logo small
Stanford University Libraries » Online resource » eResource
Updated daily, Current Contents Connect is a multidisciplinary current awareness web resource providing access to complete bibliographic information of the world's leading scholarly journals.   It provides complete tables of contents and bibliographic information, including abstracts, from about 8,000 journals, 2,000 books, and 7,000 scholarly web sites.  It includes pre-published electronic journal articles and links to the full text.   Database coverage: 1998 to the present.  For more information, please see Fact sheet, Quick Reference Card, and recorded training.
[New York] : Elsevier, 2004-
Stanford University Libraries » Online resource » eResource
"Updated daily, Scopus is the largest abstract and citation database of peer-reviewed literature. It also includes web sources, patents, articles in-press, book series, conference proceedings, and trade publications. Scopus provides international coverage of literature in science, technology, and medicine, and social sciences plus related content in the arts and humanities. 1996-present plus selected coverage back to 1823."
Stanford University Libraries » Online resource » eResource
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
Stanford University Libraries » Online resource » eResource
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 » 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) » 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-
Stanford University Libraries » Online resource » eResource
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.


[Hoboken, N.J.?] : John Wiley & Sons.
Stanford University Libraries » Online resource » eResource
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 » 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-
Stanford University Libraries » Online resource » eResource
"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."


Please also see Databases section of this guide to use mass spec databases.

Mass spectrometry handbook
Hoboken, N.J. : J. Wiley & Sons, c2012.
Stanford University Libraries » Online resource » eResource
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.
Stanford University Libraries » Online resource » eResource
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.
This authoritative book on MALDI MS (Matrix-Assisted Laser Desorption-Ionization-Mass Spectrometry), now finally available in its second edition and edited by one of its inventors, gives an in-depth description of the many different applications, along with a detailed discussion of the technology itself.Thoroughly updated and expanded, with contributions from key players in the field, this unique book provides a comprehensive overview of MALDI MS along with its possibilities and limitations. The initial chapters deal with the technology and the instrumental setup, followed by chapters on the use of MALDI MS in protein research (including proteomics.
Mass Spectral and GC Data
2nd, rev. and enl. ed. Weinheim ; New York : VCH, 1992-
SAL3 (off-campus storage) » Stacks » RS189 .P425 1992 F PT.1


Protocols & methods

Amsterdam ; Burlington, Mass. : Elsevier, c2012.
Stanford University Libraries » Online resource » eResource
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-
Stanford University Libraries » Online resource » eResource
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.
Stanford University Libraries » Online resource » eResource
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
Secaucus, NJ : Springer
Stanford University Libraries » Online resource » eResource
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.


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

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):

Stanford University Libraries » Online resource » eResource
BrowZine is an app that lets you browse, read and monitor thousands of scholarly journals available from the Stanford University Libraries. It works on these types of devices: all iPads, iPhones and iPod Touches with iOS v7.x+, Android Tablets and Smartphones with OS v4.1+ and Kindle Fire HD Tablets.  You can browse titles by subject to easily find journals of interest, create a personal bookshelf of favorite journals, be alerted when a new issue of a journal is published, save articles in your personal library.  BrowZine can easily be synced up with, Mendeley, Zotero, and other services to help keep all of your information together in one place. For installation details, please see this blog post: BrowZine table App Now Available from the Stanford Libraries