The Nature and Utility of Mass Spectra

Feb 01, 2010
Volume 2, Issue 23, pg 82–93

The phenomenal growth of mass spectrometry (MS) as a diverse analytical tool, especially when viewed from my occasional role teaching and participating in liquid chromatography–mass spectrometry (LC–MS) courses, has underscored the need for useful references: courses, books and various learning tools. Unfortunately, for some who seek to expand their knowledge of the field, a well-meaning purveyor of knowledge may unwittingly assume the student understands more than they actually do. In a recent interview, Professor Harold McNair, renowned for his book Basic GC, describes the book's genesis, which harkens back to a 1963 lecture he gave at the University of Athens, Greece. After that first lecture, he says, the faculty begged him to return the following day. After four lectures, they begged him to commit the lectures to paper. Hence, the initial draft of Basic GC. Written for Europeans for whom English is a second language, the book adopts a basic English style. "It was a simple book," says McNair, "easy to read." Eventually translated into eight languages, the book sold over 130000 copies.1 Hence, by happenstance, a sorely needed text became the basis for training at universities and the model for short courses. Almost a half-century later, we enjoy far greater access to the experience of others via the internet.

Basics of the mass spectrum: The sine qua non for practitioners is, of course, mastery of the language of MS, which takes the form of spectral output. Jim Clark, a retired chemistry teacher in the UK, has developed an accessible, comprehensive and useful resource that captures a wealth of experience from his years teaching. His website (, aimed more at beginning students than advanced ones, serves as a quick refresher for the scientist–practitioner who does not regularly use MS. Many of the examples in the first section of this column are adapted from Clark's work, updated with our current appreciation of accurate mass and atmospheric pressure ionization practice. Take from it what you will and apply as needed.

Tools of the experienced practitioner: We have seen various software tools used to search for an unambiguous answer to what a spectrum represents. James Little ( provides some insight to using the tools and how he approaches problem solving.

Deriving the unambiguous answer: Defining the unique qualities of the spectrum gives us a basis for de novo assessments. As comfortable as we can be with the fidelity of isotope prediction, it does not mean we can apply rules to flawlessly derive the only possible unambiguous formula from an acquired ion. Kirsten Hobby (see worked to develop a software tool (referred to as i-FIT in MassLynx software, Waters Corp., Milford, Massachusetts, USA) to compare an acquired spectrum with its theoretical equivalent. Hobby's comments from a few years ago on the limits and utility of what he designed to help derive an answer are compared with thoughts from Richard Denny, current architect of MassLynx spectral "fitting" tools.

The Molecular Ion (M + ) Peak

The formation of molecular ions: In common applications of electron ionization (EI), a flash-vaporized organic sample passes into the ionization chamber to encounter a stream of 70 eV electrons. These electrons are highly energetic, enough so to snatch an electron from the outer shell of an organic molecule. In so doing, they form a positive ion (radical cation), a molecular ion. When ionization occurs in atmospheric techniques such as electrospray (ESI) — albeit by very different mechanisms — this ion is called the pseudomolecular ion (M+H) after forming by adding a proton (rather than extracting an electron). The resulting ion can also be referred to as the parent ion or, in more modern usage, the precursor ion, when the ion is the first step in a fragmentation experiment such as MS–MS.

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