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Mass Spec Missive

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The generally fine article on mass spectrometry in the June issue of Genome Technology (“A Spectrum of Choices,” p. 50) had several technically incorrect statements that I’d like to bring to your attention.

First, the author confuses the ionization of proteins vs. peptides in the article. Most proteomics studies done via mass spec involve the digestion of proteins into peptides, followed by the mass analysis of the peptides produced by the protein digest.

Also, the description of a peptide-mass-fingerprinting on p. 54 should say, “A pulse laser shoots the samples and vaporizes and ionizes the peptides,” not proteins.

On p. 52 the author confuses identification of a protein by its molecular weight with the identification of a protein by its peptide map. The article states: “...researchers used a MALDI coupled with a single time-of-flight analyzer to first try to identify proteins by molecular weight, matching them with one in the databases.” The identification is done by matching the molecular weight of the peptide ions produced from a protein digest, not from the molecular weight of the protein as is implied in the paragraph.

Also on p. 52 the author wrote: “...each has at least one mass analyzer that applies an electromagnetic field to the resulting ions and sorts them by mass.” A linear time-of-flight mass spectrometer does not apply an electromagnetic field; it separates ions on the flight time of ions after they are accelerated by a high voltage.

It is unfortunate that one of the newest ion sources designed for proteomics, atmospheric pressure (AP) MALDI, gets only a one-line mention on p. 55. When combined with an ion trap analyzer, an AP-MALDI Ion Trap can produce data (both MS and MS/MS) similar to that generated by a much more expensive MALDI-TOF/TOF spectrometer. Data acquisition rates and sensitivity levels are similar. The major differences are less MS/MS fragmentation and lower mass accuracy produced by the ion trap. A benefit of the AP-MALDI system is that the MALDI source can rapidly (in about five minutes) be replaced with an ESI ion source. This gives the user the capability of using the mass spectrometer with either a MALDI or ESI ion source.

John Michnowicz, PhD
Proteomics Program Manager
Life Sciences and Chemical Analysis
Agilent Technologies

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