Sensitivity is a key attribute of mass spectrometers to allow quantification of minute amounts of analytes. Yet this sensitivity can be a conundrum. Myriad sources can contribute contaminants that can impact background and confound interpretation of results. An increased background signal can make it challenging to detect molecules of interest.

There are two broad categories of mass spectrometry (MS) – organic and atomic. In the case of organic or molecular MS, such as LC-MS, the major contamination concern is unwanted organic molecules. Atomic MS or ICP-MS (Inductively Coupled Plasma MS) is typically used to measure metal content of different substances. Therefore metal contaminants are the prime worry. And in mass cytometry, an MS technique based on ICP-MS and TOF-MS (Time-of-flight MS) used for the determination of the properties of cells, both metal and organic contamination can affect results.

In a 2018 article in LCGC North America, Dwight Stoll, PhD, professor in chemistry, Gustavus Adolphus College, warns that every step in the analysis presents potential for introducing contaminants, and that work habits must be developed that at least minimize problems with contamination, even if it is effectively impossible to eliminate them completely (1).

Environmental Contaminants

Organic contaminants or metal particles from laboratory air or simply dust can dissolve in open solvent or sample containers. ICP-MS requires low detection limits to detect metal contamination and impurities, particularly in the semiconductor industry. For this reason, Class 100 clean rooms are used for sensitive operations.


MS operators can shed contaminants from skin, hair or even protective gloves that have come into contact with lunches, phones or other laboratory instruments or surfaces. Attention to hygiene and the appropriate personal protective wear limit contaminating particles that can be generated or distributed from the human body. For LC-MS Stoll recommends wearing nitrile gloves when handling instrument components, filling solvent bottles, and preparing samples (1).

Sample-to-Sample Transfer

Certain sample components, both metal and organic, can be sticky and may need to be addressed. These components can contaminate sample introduction systems, solvent inlet filters, lines or tubing and cross contaminate sequential samples.

In ICP-MS, blanks are used to monitor cross contamination. Blanks undergo all the same operations in parallel as samples, albeit minus sample, and are used between samples, or before and after similar sequential sample runs, to qualify wash-out protocols.

Detergents and Leaching

Use dedicated solvent bottles for LC–MS. Assign specific bottles to specific instruments and solvents, and do not wash with detergent. The risk of contaminating mobile phases with residual detergent is simply too great (1). In ICP-MS preferably use HDPP (high density polypropylene) containers and vials since lead can leach from glass and contaminate runs. Optionally, use elementally-pure glass ware. In the semiconductor industry Teflon is the material of choice.


In ICP-MS only use deionized (DIW) or distilled-deionized (DDIW) water of greater than 18.2 megaohm resistance. All acids and solvents need to be of ultrapure grade, ICP-MS grade, meaning extremely low levels of metal contamination.

In LC-MS there can be solvent impurities, compounds related to microbial growth in solvent reservoirs or that leach from membrane filters during solvent filtration or from solvent bottle covers. In addition, Stoll advises to use mobile-phase additives with great care. In principle, additives that are marketed for LC–MS applications should be both free from particulates and free from contaminants that might enhance or suppress ionization of analytes of interest (1).

He stresses to compare additives from different sources when developing a new method and to take all necessary steps to prevent microbial growth in mobile-phase bottles and LC system solvent line components. Potential steps include frequent emptying and filling of solvents, adding low levels of organic solvent to aqueous mobile phases, and flushing instrument solvent lines and components with organic solvent if the instrument is not used for an extended period (1).

One of the challenges for people who are crossing from one MS field to another, is changing their perception and habits. For example, low Total Organic Content (TOC) does not mean low elemental contamination. In fact, often the low TOC reagents are in glass bottles, a no-no for ICP-MS experiment.

This brief introduction to sources of contamination in MS is far from exhaustive. To optimize performance of today’s sensitive MS instrumentation great care must be taken to avoid contaminating the system with interfering compounds. The experts’ advice is to adopt best practices that minimize the potential for contamination.


Resources (May require registration)

LC-MS, GC-MS and others: ChromatographyForum

ICP-MS: PlasmaChem

Mass cytometry:  Cytoforum



1. LCGC North America-08-01-2018, Volume 36, Issue 8, Pages: 498–504

Previous articleVaccine Study Explores COVID-19 and Autoimmune Disease
Next articleResearchers Discover the Power behind Innate Lymphoid Cells