Common Mass Spectrometry Contaminants and their Sources

Mass Spec

The contaminant information below is taken from "Interferences and contaminants encountered in modern mass spectrometry" Bernd O. Keller, Jie Sui, Alex B. Young and Randy M. Whittal Analytica Chimica Acta  627, Issue 1, 3 October 2008, Pages 71-81


List of Positive Ion Contaminants (download PDF)
List of Negative Ion Contaminants
 (download PDF)
List of Repeating Unit Contaminants (download PDF)
List of Adducts, Losses, and Replacements (download PDF)
List of Solvent Masses (download PDF)
References for Above Contaminants (download PDF)
Glossary for Contaminant Tables above (download PDF)

Salt and Detergent Tolerances for MALDI, ESI (download PDF)


"Mass spectrometrists have always been plagued by spurious peaks in their spectra resulting from contaminants that should not be present in an ideal lab. Unfortunately, that type of lab does not exist in the sense that impurities are generally present in the air, in reagents, in lab ware and in the samples themselves. So, the best way to cope with them is to be aware of their existence and, in some cases, to make use of them as internal calibrants.

At one stage, during the era of domination by electron ionisation, chemical ionisation and fast atom bombardment mass spectrometry, the interferents and contaminants were fairly well documented. Then along came the 1990s and the new techniques of electrospray ionisation and matrix-assisted laser desorption/ionisation (MALDI) which unveiled new types of interfering compounds that were not a problem in the traditional methods. This was compounded by the trend towards miniaturized techniques which multiply the effects of background ions during sample handling and analysis.

As these modern mass spectrometry techniques took hold, individual labs began to recognize their own regular contaminants and information leaked into the published literature, building up as the techniques became more widespread. This information is widely dispersed over many sources and access is difficult. Recognising this, scientists in Canada have pulled much of it together into one publication, supplementing it with data on interferences encountered in their own labs over the last ten years. Even more helpfully, they have compiled a database containing the essential data on more than 650 contaminants.

Bernd Keller from the University of British Columbia, with Jie Sui, Alex Yung and Randy Whittal from Queen's University, Kingston and the universities of Toronto and Alberta, respectively, published their summary in Analytica Chimica Acta (July 2008). They separated their interferences into two categories, proteinaceous and non-proteinaceous.

Many potential proteinaceous interferences arise from the enzymes used to digest the protein(s) of interest into smaller fragments for analysis. In practice, the enzyme is present at greater concentrations than the target protein, so the autolysis products of the enzyme can become significant. Keller recommends blank testing of enzyme autolysis. The advent of enzyme-less digestion procedures such as microwave-assisted hydrolysis will begin to alleviate this problem.

Other protein-based interferences arise from involuntary contamination from external sources, such as keratins from discarded skin cells. They are found in dust and may not be solely of human origin, especially in labs performing animal studies. The need to be ceaselessly vigilant was illustrated by the sudden appearance of sheep keratins during a study of mouse proteins. They were eventually traced to a new woollen sweater that a team member had begun to wear.

Other external protein interferences include those used in immunoassays such as bovine serum albumin and the immunoglobulins. They can often overpower signals from the target analytes unless attempts are made to remove them by gel electrophoresis or HPLC.

A third category of proteinaceous interferences was identified as those originating from non-specific fragmentation of peptides within the ion source. These fragmentations can be reduced by changing the instrumental parameters. Conversely, they can be amplified to carry out multiple-stage mass spectrometry experiments if required.

The non-proteinaceous interferences were summarised in three categories. The first relates strictly to the formation of clusters from matrix compounds used in MALDI mass spectrometry. Their formation and detection are relatively easy and means for preventing their occurrence in the first place are outlined.

The second category concerns the formation of adducts that are formed by interaction with solvent molecules or ions such as potassium or the ubiquitous sodium ion. In some cases, their formation is encouraged because they can increase the ionisation efficiency of certain compounds. Other adduct ions have been observed from components of the silicone oils used in diffusion pumps.

Polymeric interferences from plastic labware are also very common but they can also originate from detergents that are deliberately added during sample preparation. These can generally be distinguished in mass spectra by the appearance of repeating units. In the third category, the authors discuss plasticisers such as phthalates and other general interferences that have been reported in the literature.

The contaminants database that the researchers complied is in an Excel spreadsheet available via the supplemental information of their publication. It lists the accurate monoisotopic positive ions of more than 650 species as well as the negative ions of those that were reported in the literature. Common repeating units of polymeric or adduct interferences, common adducts, common solvents and a list of the published references are also included.

Clearly such a list can never be complete but the database provides a detailed and valuable reference tool that can be updated as new interferences and contaminants are defined."

"Interferences and contaminants encountered in modern mass spectrometry" Bernd O. Keller, Jie Sui, Alex B. Young and Randy M. Whittal Analytica Chimica Acta  627, Issue 1, 3 October 2008, Pages 71-81 Article