JEOL USA blog

How Does Field Ionization Work?

Fri, 27 Feb 2026 10:12:34 GMT

What Role Does Chemical Ionization Play in GC-MS?

Thu, 15 Jan 2026 14:52:58 GMT

What Role Does Chemical Ionization Play in GC-MS?

Gas chromatography–mass spectrometry, commonly abbreviated as GC-MS, is designed to determine what chemical species are present in a sample. By coupling chromatographic separation with mass-based detection, GC-MS enables analysts to resolve complex mixtures, like environmental samples, petrochemical fractions, or biological extracts, and assign identities to individual volatile and semi-volatile components. In many workflows, GC-MS identification relies on a combination of chromatographic behavior and mass spectral data to effectively distinguish compounds. For known substances, comparison against established reference libraries is often sufficient. The analytical challenges increase, however, when GC-MS is applied to unknown compounds, newly synthesized materials, or trace-level contaminants that fall outside existing databases. Under these conditions, identification hinges on a more fundamental requirement: establishing the intact molecular mass. Chemical ionization, also abbreviated as CI, can provide this critical information through preserving molecular ions, allowing GC-MS to move beyond pattern matching and toward reliable molecular confirmation.

How Chemical Ionization Controls Energy Transfer in GC-MS

Chemical ionization introduces a different ionization environment within the GC-MS ion source, deliberately designed to control how energy is transferred to analyte molecules. Instead of interacting directly with the analyte, ionization occurs through a reagent gas that acts as an intermediary. Methane, isobutane, and ammonia are commonly selected because they form stable, predictable reagent ions under controlled-source conditions.

Ionization begins with the reagent gas itself. Once ionized, the reagent ions establish a low-energy chemical environment inside the ion source. As neutral analyte molecules enter this region, they undergo ion-molecule reactions, such as proton transfer or adduct formation. Because the analyte is ionized indirectly, the amount of internal energy transferred during the process is tightly constrained.

The analytical impact of this controlled energy transfer is immediate. Molecular bonds are largely preserved, fragmentation is minimized, and the resulting GC-MS spectrum is dominated by a clearly defined molecular ion. Rather than producing dense fragmentation patterns, CI concentrates signal intensity into ions that directly reflect molecular weight. For compounds where molecular mass information is difficult to obtain using more energetic ionization methods, such as electron ionization (EI) or CI, CI provides a clear path to molecular confirmation because it can preserve the intact molecular ion rather than promote extensive fragmentation.

Chemical Ionization as a Mass Verification Tool in GC-MS

In GC-MS workflows, CI is applied to confirm molecular weight. Standard GC-MS conditions generate structurally informative fragmentation patterns, but the energetic nature of these processes can suppress the molecular ion, particularly for thermally labile or highly substituted compounds. Without a clearly observable molecular ion, identification becomes more uncertain and increasingly reliant on indirect evidence.

Chemical ionization addresses such a limitation by preserving molecular integrity during ion formation. Rather than distributing ion signal across numerous fragment ions, the technique concentrates intensity into a small number of species that directly reflect molecular mass, most commonly a protonated molecule or a predictable adduct. This focused spectral output provides clear molecular weight information, especially when reference library matching alone is insufficient.

Beyond molecular weight confirmation, CI also enhances interpretability in demanding GC-MS applications. Cleaner spectra reduce ambiguity during data processing, support more robust spectral deconvolution, and improve discrimination between closely related compounds. For samples containing coeluting components or structurally similar species, this clarity strengthens identification decisions and reduces the likelihood of misassignment.

Enabling Accurate Mass and Elemental Formula Determination

High-resolution GC-MS places additional demands on ionization strategy, as accurate mass measurements are only meaningful when the correct molecular ion is first established. Without clear molecular ion information, even high mass accuracy cannot resolve structural uncertainty. Chemical ionization preserves the molecular ion, allowing the correct nominal mass to be established before exact mass calculations are applied.

With the molecular ion confirmed, mass data can be interpreted with confidence to evaluate plausible elemental compositions. Subtle mass differences can become analytically significant, enabling discrimination between closely related formulas such as CxHyNz variants that may otherwise appear indistinguishable. This capability is particularly important in research, regulatory, and forensic contexts, where compounds may be novel, intentionally modified, or designed to resemble known substances.

By supporting reliable formulate determination, CI extends the role of GC-MS beyond library-based identification to definitive molecular characterization and increases the confidence of analytical conclusions for compounds that cannot be resolved by spectral matching alone.

Selective Detection Using Negative Chemical Ionization in GC-MS

Chemical ionization also enables a highly selective GC-MS approach known as negative chemical ionization, or NCI. In NCI, the ion source favors electron capture over proton transfer, allowing only compounds with sufficient electron affinity to form stable negative ions. This selectivity is governed by chemical structure rather than broad ionization efficiency. Halogenated and nitro-containing compounds respond strongly to NCI, while most background species remain neutral. As a result, NCI GC-MS delivers high sensitivity with minimal chemical noise, which is particularly advantageous for trace-level analysis in complex sample matrices.

Applying Chemical Ionization with JEOL USA

The role of chemical ionization in GC-MS is to confirm molecular weight, improve spectral clarity, and enable selective detection strategies when conventional approaches reach their limits. Its capabilities enable GC-MS to progress from tentative identification to definitive molecular characterization, even for unknown, trace-level, or structurally similar compounds. JEOL USA offers GC-MS systems with the flexibility required to apply chemical ionization effectively, enabling smooth transitions between ionization modes to accommodate different analytical objectives. Platforms such as the JMS-T2000GC AccuTOF™ GC-Alpha 2.0, the JMS-Q1600GC UltraQuad™ SQ-Zeta, and the JMS-TQ4000GC combine robust performance with advanced ionization support, extending the abilities of GC-MS for demanding analyses. To learn more about how JEOL USA's GC-MS solutions can support precise molecular identification in your laboratory, speak with a specialist from JEOL USA today.

An Overview of Different GC-MS Ionization Techniques

Mon, 28 Jul 2025 23:13:00 GMT

An Overview of Different GC-MS Ionization Techniques

Chemical ionization, sometimes called CI, is increasingly important in analytical chemistry. It represents a gentler approach than traditional counterparts like electron ionization (EI). EI, in particular, is characterized by an aggressive ionization mechanism that often results in extensive fragmentation of the analyte molecules. This fragmentation can be useful for identifying a molecule, however, sometimes the molecular ion is not present. Therefore, using softer ionization techniques for gas chromatography-mass spectrometry (GC-MS) applications, such as CI, field ionization (FI), and photoionization (PI), produce the molecular ion for easier identification.

The CI Process: A Closer Look

Chemical ionization takes place in an ion source operating at relatively high pressures (0.1-1 Torr). The process begins with the introduction of an ionizing gas (e.g., methane, isobutane, ammonia) into this high-pressure environment. The gas is first subjected to a high-energy electron beam, leading to the formation of reagent ions. These ions, in turn, engage in ion-molecule reactions with the analyte molecules present. Through this interaction, a proton (or another suitable ion) is transferred to the analyte, culminating in the generation of molecular ions that closely reflect the original molecular structure of the analyte with minimal fragmentation.

Advantages of CI

The foremost advantage of chemical ionization lies in its soft ionization characteristic, which ensures the generation of intact molecular ions. This is particularly beneficial when analyzing large, fragile molecules that are susceptible to fragmentation under the harsh conditions of electron ionization (EI). Consequently, CI facilitates a more straightforward determination of molecular weights and, by extension, the molecular structure of the analyte. Its application spans diverse fields, including environmental analysis, forensics, and pharmaceutical research, underscoring its versatility and efficacy in handling complex analytical demands.

Alternatives to CI Techniques

While CI serves as the foundational technique, several variations have been developed to cater to specific analytical needs. These include field ionization (FI), photoionization (PI), and electron ionization (EI), each distinguished by its ionization mechanism and the type of analytes it is best suited for.

Field Ionization (FI)

Field ionization is a technique that employs a high electric field to ionize molecules without necessitating a collisional process. The electric field facilitates the removal of electrons from the analytes, leading to ion formation. FI is particularly useful for the analysis of high molecular weight and thermally labile compounds that might not withstand the energy requirements of other ionization methods. FI is the most soft ionization option of all the options for GC-MS applications.

Photoionization (PI)

Photoionization utilizes ultraviolet (UV) or visible light photons to eject electrons from molecules, thereby ionizing them. The energy of the photon is a critical factor, as it must exceed the ionization potential of the molecule for ionization to occur. PI's selectivity and the ability to control the photon energy make it a valuable tool for the analysis of a wide range of organic and inorganic compounds that contain a chromophore.

Electron Ionization (EI)

Electron ionization, one of the most widely used techniques, involves bombarding analyte molecules with high-energy electrons. This process not only ionizes the molecules but also induces fragmentation, which, while offering detailed structural information, can complicate the analysis of molecular weights. EI's utility lies in its robustness and the extensive database of EI spectra available for compound identification.

Closing Thoughts

Chemical ionization, with its soft ionization approach, stands out as a vital technique in the arsenal of mass spectrometry. By generating molecular ions with minimal fragmentation, CI facilitates a clearer understanding of molecular weights and structures, proving indispensable in various scientific fields. The evolution of CI into specialized techniques like FI, PI, and EI further broadens its applicability, ensuring its continued relevance in advancing analytical chemistry. As we delve deeper into the complexities of chemical analysis, the role of CI and its derivatives becomes increasingly pivotal, offering nuanced insights into the molecular intricacies of the substances that define and sustain the natural and synthetic worlds.

Adhesives: Key Applications of Polymer Identification

Mon, 21 Jul 2025 15:51:00 GMT

Adhesives: Key Applications of Polymer Identification

The modern industrial landscape showcases a myriad of applications for adhesives, ranging from simple household uses to complex automotive and aerospace applications. At the heart of enhancing performance and ensuring quality control lies the intricate science of polymer identification.

This blog post delves into the critical role of polymer identification in the deformulation and quality control of adhesives. Another focus will be on related advanced analytical techniques, including gas chromatography-mass spectrometry (GC-MS) and Direct Analysis in Real Time-Mass Spectrometry (DART-MS).

Deformulation and Quality Control: A Precursor to Innovation

Deformulation, the process of breaking down and analyzing the composition of adhesives, is pivotal in understanding and improving adhesive formulations.

Through polymer identification, manufacturers can reverse-engineer products for quality control, patent infringement avoidance, and competitive analysis. Techniques like GC-MS, including the UltraQuad™ SQ-Zeta and GC-Alpha, and DART-MS, such as the AccuTOF DART, are instrumental in this analysis. They offer a wide range of detailed insights into the molecular structure and composition of adhesives.

Enhancing Performance through Pyrolysis-GC-MS

The application of pyrolysis-GC-MS, especially when integrated with the Frontier Lab pyrolyzer and msFineAnalysis AI, represents a leap forward in adhesive analysis. This method uses high temperatures to allow for the thermal decomposition of complex polymers into simpler molecules. These are then analyzed using GC-HRTOFMS, which has an extended time-of-flight mass analyzer capable of high-resolving power (> 30,000 FWHM) and excellent accurate mass accuracy (> 1 ppm). Data processing is then carried out by msFineAnalysis AI, a next-generation software that adds structure analysis capability to improve the overall automatic qualitative analysis functionality. This combines GC/EI high-resolution data, GC/soft ionization high resolution data, and structure analysis tools using three AIs. These advanced AI technologies allow msFineAnalysis AI to provide an unique automatic structure analysis capability that was not previously available for GC-MS qualitative analysis.

Competitive Analysis and Product Development

In the highly competitive adhesives market, the ability to analyze and compare products is invaluable. This is why polymer identification and the use of polymer identification tests are so important.

Advanced analytical methods provide a comprehensive understanding of an adhesive's composition, which can be used to enhance product performance, adherence, and durability. These insights are essential for developing new formulations that meet or exceed industry standards and consumer expectations.

Quality Control and Regulatory Compliance

Quality control is paramount in the production of adhesives. Accurate polymer identification ensures that raw materials and the final product meet stringent industry and regulatory standards.

Techniques like DART-MS facilitate the rapid, non-destructive analysis of adhesives, enabling real-time quality control during manufacturing. This not only ensures the consistency and reliability of adhesive products but also aids in regulatory compliance by verifying the absence of prohibited substances.

Interested in Polymer Identification Tests?

The field of polymer identification in adhesives is a testament to the synergy between chemistry and technology. By employing sophisticated analytical techniques, such as GC-MS and DART-MS, the adhesives industry can achieve greater heights in product performance, safety, and innovation.

As the demand for more robust, efficient, and environmentally friendly adhesives grow, the role of polymer identification tests will become imperative in meeting these challenges.

Through continuous research and technological advancements, the potential for creating next-generation adhesives that are tailor-made for specific applications is within reach. By improving polymer identification tests, adhesives will remain of high-quality.

Join JEOL USA at Pittcon this year and discover the forefront of analytical instrumentation!

Now that you understand the key applications of polymer identification, we would like to take a moment to invite you to see us at Pittcon.

At Pittcon, you can engage with our experts, experience live demonstrations, and learn how our cutting-edge technology can elevate your work.

Whether you're delving into materials science, pharmaceuticals, or environmental analysis, JEOL is committed to advancing your discoveries. Don't miss this opportunity to connect with us and explore how we can support your scientific endeavors. See you at Pittcon!

What Analyzers are Used for Polymer Identification?

Mon, 01 Apr 2024 19:19:00 GMT

What Analyzers are Used for Polymer Identification?

In the ever-evolving field of polymer science, the accurate identification and analysis of polymers are critical for quality control, research, and development. This blog will delve into the sophisticated analytical techniques used for polymer identification and highlight the principles, applications, and limitations of different polymer analysis techniques.

Pyrolysis Gas Chromatography-Mass Spectrometry

A crucial analytical tool that can be used for polymer identification is pyrolysis gas chromatography-mass spectrometry (Py-GC-MS).

This technique involves the thermal decomposition of the polymer (pyrolysis), followed by the separation and identification of the resulting compounds.

Frontier lab pyrolyzers are commonly used and paired with JEOL's Q1600GC or GC-Alpha. The msFineAnalysis AI software enhances the process by providing sophisticated data interpretation, leveraging artificial intelligence to analyze complex pyrolysis results. This method is particularly effective for identifying unknown polymers, additives, and fillers, and for understanding their thermal degradation behaviors.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Another essential instrument in polymer characterization is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

JEOL’s SpiralTOF, coupled with msRepeatFinder software, offers high-resolution mass spectra of polymers. This technique excels in determining molecular weights and distribution, end-group analysis, and copolymer composition.

However, it is crucial to note that as the molecular weight of a polymer increases, the oligomeric resolution declines. Eventually, it will render MALDI-TOF MS unsuitable for identifying the polymer. Only the molecular weight can be determined beyond this threshold, which varies depending on the polymer type.

Nuclear Magnetic Resonance Spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy is another versatile tool used for polymer identification. It provides detailed information about the molecular structure, including the arrangement of atoms within the polymer.

This non-destructive technique can differentiate between crystalline and amorphous regions in polymers and is instrumental in elucidating copolymer composition and sequence distribution. NMR is particularly useful for understanding the chemical structure and physical properties of polymers.

Meet us at Pittcon

The field of polymer science relies heavily on advanced analytical techniques for polymer identification. Each method, Py-GC-MS, MALDI-TOF MS, and NMR, offers unique advantages and limitations. Their application is pivotal in ensuring the quality and performance of polymer materials, contributing significantly to advancements in materials science and engineering.

At JEOL, we are continually inspired by the endless possibilities of polymer science and the critical role of different analysis techniques for driving innovation. These tools are crucial for successfully identifying polymers.

As we explore the frontiers of material characterization, we invite fellow experts and curious minds to join us at our booth at Pittcon this year. This is an excellent opportunity for you to engage with our team, discover our latest advancements in polymer analysis, and discuss how our cutting-edge technologies can empower your research and development endeavors.

Together, let's shape the future of polymer science and uncover the next breakthrough in material technology. We look forward to insightful conversations and collaborations with you at Pittcon.

References

Kusch P. Pyrolysis-Gas Chromatography: Mass Spectrometry Of Polymeric Materials. Singapore: World Scientific Publishing Company; 2018.
Lattimer R, Montaudo G. Mass Spectrometry of Polymers. USA: CRC Press; 2001.
Tonelli A. NMR Spectroscopy and Polymer Microstructure: The Conformational Connection. USA: Wiley-VCH; 1989.
Stuart B. Infrared Spectroscopy: Fundamentals and Applications. USA: Wiley; 2004.

Unlocking Material Characterization with Pyrolysis-GC-MS: Key Takeaways from Our Recent Webinar

Thu, 02 Nov 2023 21:54:49 GMT

Explore the Future of Petrochemical Analysis with Our Updated Brochure

Thu, 26 Oct 2023 04:01:00 GMT

In the realm of scientific inquiry, staying ahead of the curve is essential for breakthroughs. Our newly updated brochure, "JMS-T2000GC AccuTOF™ GC-Alpha Petroleum and Petrochemical Solutions," serves as your compass to navigate the intricate world of petrochemical analysis. Tailored for seasoned researchers and emerging scientists alike, this comprehensive resource delves into specific analytical techniques for applying mass spectrometry to petrochemical analysis.

Introduction to Petrochemical Exploration:

The brochure kicks off with an exploration of the world of petrochemical analysis, highlighting its importance in diverse industries. Whether you're seeking to understand hydrocarbon structures or decode complex mixtures, this section sets the stage for a profound learning journey.

The Power of Soft Ionization Techniques:

Delve into the heart of soft ionization techniques like Field Ionization (FI) and Field Desorption (FD). Discover how these techniques create minimal fragmentation, allowing scientists to generate molecular ions for comprehensive insights. This section unveils how these techniques revolutionize the study of hydrocarbon composition.

Mapping Complexities: Group-Type Analysis without GC Separation:

Uncover the ingenious technique that sidesteps the need for GC separation while providing in-depth group-type analysis. Dive into how the AccuTOF™ GC-Alpha's high mass resolution and soft ionization capabilities simplify the process, unveiling a wealth of insights without the complexities of chromatography.

One-Dimensional and Two-Dimensional GC Techniques:

Explore a spectrum of GC conditions, from ultra-high separation with long columns to fast separation with short ones. This section also introduces the revolutionary Comprehensive Two-Dimensional Gas Chromatography (GCxGC) technique, showcasing its unparalleled capacity for detailed hydrocarbon analysis.

Mastering Complexities: Crude Oil Analysis:

Unravel the intricate world of crude oil analysis through various ionization methods. Discover how these methods allow scientists to extract comprehensive group-type information and unveil structural insights. This section guides you through the process of gaining multifaceted insights from this complex mixture.

Unlocking Insights: msRepeatFinder and msFineAnalysis AI:

Learn about the power of data visualization and automated peak detection with msRepeatFinder and msFineAnalysis AI. This section showcases how these tools amplify your ability to analyze highly complex hydrocarbon mixtures, offering deeper insights with ease.

Discover the Guide

In your pursuit of analytical excellence and uncharted knowledge, our brochure "JMS-T2000GC AccuTOF™ GC-Alpha Petroleum and Petrochemical Solutions" is your compass, guiding you through the complexities of petrochemical analysis.

Don't miss out on this opportunity to revolutionize your research. Download the brochure now and pave the way for discovery, innovation, and a deeper understanding of petrochemical analysis: (URL)

Explore the Future of Petrochemical Analysis with Our Updated Brochure

Thu, 28 Sep 2023 04:01:00 GMT

ACS Fall 2023 In Review

Wed, 13 Sep 2023 00:56:23 GMT

Why GC-MS is Ideal for Real-Time Process Gas Analysis

Thu, 10 Aug 2023 09:03:50 GMT

Streamlining Process Gas Monitoring with Mass Spectrometry

Thu, 10 Aug 2023 08:55:57 GMT

5 Different Mass Spectrometer Techniques

Thu, 10 Aug 2023 08:34:36 GMT

How GC Mass Spectrometry Enhances the Study of Organic Compounds

Thu, 03 Aug 2023 15:54:08 GMT

A Complete Guide to Mass Spectrometers

Tue, 18 Jul 2023 08:22:27 GMT

In-source fragmentation part one. “Breaking up is (not so) hard to do.”

Wed, 10 May 2023 18:32:09 GMT

Introduction

In the preceding segment of this series, we found out that our “unknown” has the elemental composition C₈H₁₁N₄O₂. However, that’s not sufficient to identify the compound because there are many possible chemical structures (isomers) that can have the same elemental composition. We can use fragment ions to distinguish many isomers. Here, let’s discuss in-source fragmentation in depth.

Distinguishing Between Isomers

We can’t base a chemical analysis of a pure compound on elemental composition alone. Let’s suppose that we determine that a sample found in a suspect’s car contains a molecule with the elemental composition C₁₇H₁₉NO₃. It could be morphine – but let’s not break out the handcuffs yet! It could be one of several drug isomers that have the composition C₁₇H₁₉NO₃ such as hydromorphone or norcodeine. It could also be another isomer – piperine, the spicy molecule in black pepper! Clearly, we need a way to distinguish between isomers.

In traditional gas chromatography coupled with mass spectrometry (GC-MS) the electron ionization (EI) mass spectra have fragment-ion peaks that we can search against databases to identify compounds. How can we get fragment-ion data for compounds analyzed with soft ionization methods like DART-MS?

Collision-induced dissociation

The most common way to break apart ions in a mass spectrometer (in-source fragmentation) is to use an electric field to accelerate the ions and collide them with gas molecules in a partial vacuum. This is called collision-induced dissociation (CID) which is the basis for tandem mass spectrometry (MS/MS) in mass spectrometers like the JEOL TQ4000 triple quadrupole mass spectrometer system.

One of the simplest ways to implement CID is to fragment the ions in the interface between atmospheric pressure and vacuum, referred to as “in-source CID” or “cone voltage CID”. To understand how this works, let’s take a closer look at how ions in a gas stream at atmospheric pressure are introduced into the vacuum system of the mass spectrometer. There are many different designs for atmospheric pressure interfaces for mass spectrometers. The AccuTOF-DART mass spectrometer has one of the simplest and most robust designs.

The figure below shows a schematic of atmospheric pressure interface for the AccuTOF-DART mass spectrometer. The DART gas stream passes through a small hole in the first skimmer (“Orifice 1”) into a region that is evacuated by a mechanical roughing pump. Ions are directed by the electric field through a ring lens and into a small hole in a second skimmer (“Orifice 2”). A bent quadrupole ion guide transports the ions further into the vacuum system and the time-of-flight mass analyzer. The off-axis skimmer design blocks contamination from entering the ion guide and mass analyzer.

The important parameter is the potential difference between Orifice 1 and Orifice 2. If this value (the “Orifice 1 Potential” or “cone voltage”) is small – for example 20 Volts – then ions will drift through the partial vacuum region without undergoing strong collisions with gas molecules. If we increase the potential difference to say, 90 Volts, then ions will collide with gas molecules with enough kinetic energy to form fragment ions.

How about the morphine/black pepper example? The 90V fragmentation patterns for the two isomers are quite different!

Coming back to our caffeine example, here are the positive-ion DART-MS mass spectra for two different Orifice 1 potentials. The in source fragmentation of Orifice 1 = 90V spectrum are distinctive and can be related to the structure of caffeine.

Conclusion

In-source collision-induced dissociation (CID) is a simple way to generate fragment ions that can distinguish between many isomers. In the next segment of this discussion, we will consider the effect of changing the collision energy on the measured mass spectra.

To learn more about JEOL mass spectrometers and the AccuTOF-DART system, please visit us here.

How DART isotope measurements assist in elemental composition measurements

Wed, 03 May 2023 19:07:03 GMT

A deeper dive into elemental composition determination with DART

Wed, 26 Apr 2023 21:09:00 GMT

How DART mass spectrometry uncovers elemental compositions

Wed, 19 Apr 2023 13:46:04 GMT

If we have accurate mass data, DART-MS can tell us more than the molecular weight of a molecule. Let’s see how to determine the elemental composition from accurate-mass DART-MS data.

Note: The next few articles focus on the interpretation of accurate-mass spectra. Although I am using a DART-MS example, the information here applies to any data from an accurate-mass mass spectrometer, such as the JEOL AccuTOF GC-Alpha. We’ll come back to DART-MS shortly.

Elemental composition determination from an accurate mass

The first step in determining an elemental composition from an accurate mass is to specify a set of elements that might be present and set some limits on the minimum and maximum number of each element that might be present. We’ll use the caffeine example from the previous posts. Let’s assume that we know that we don’t know that the compound is caffeine, but that the compound only contains carbon, hydrogen, nitrogen and oxygen. Because accurate mass measurements are not always exactly correct, let us also assume that the measured m/z is 195.0899 instead of the exact calculated value of 195.0882. We can set the element limits based on the maximum number of each element that could give a molecular weight less than 195.

Element	Symbol	Maximum
Carbon	C	16
Hydrogen	H	34
Oxygen	O	12
Nitrogen	N	14

Next, we specify an error tolerance of 5 millimass units (5 mmu) for the accurate mass measurement. That’s 0.005 u, a bit wider than the error we expect, but wide enough that we won’t miss any possible compositions. Software then calculates the weight (actually, the m/z) for all possible combinations of the elements within the specified limits and only reports those elemental compositions that have a calculated m/z within 5 mmu. There are nine compositions that fit those constraints.

Here’s a summary of the process:

What does DBE mean, and how do we know that the correct elemental composition for the m/z 195.0899 peak is C₈H₁₁N₄O₂ instead of one of the other 8 compositions? Stay tuned for the next piece in this series!

Accurate mass information obtained with DART-MS can be used with to determine the elemental composition of molecules. You can read more about how elemental compositions are determined from accurate-mass data here. To learn more about JEOL mass spectrometers and the AccuTOF-DART system, please visit us here.

How DART mass spectrometry uncovers molecular weight information

Wed, 12 Apr 2023 18:23:41 GMT

This post describes the first piece of information we get from ambient ionization and DART-MS: the molecular weight.

How DART examines molecular weight

In the previous blog, I explained how positive-ion DART-MS can form protonated molecules [M + H]⁺ for compounds like caffeine. Here is the DART-MS caffeine mass spectrum again, with the caffeine structure and elemental composition:

Positive-ion DART mass spectrum of caffeine measured on the JEOL AccuTOF-DART system

Mass spectrometers measure the mass-to-charge ratio (symbol “m/z”). DART-MS only produces single-charge ions, so for the purpose of this discussion we can ignore the charge.

The exact masses in unified atomic mass units (u) of the most abundant stable isotopes of the elements carbon, hydrogen, oxygen, and nitrogen are:

¹²C: 12.000000
¹H: 1.007825
¹⁶O: 15.994915
¹⁴N: 14.003074

We measured the protonated molecule, so the peak at m/z 195.088 tells us that the molecular weight of the compound must be m/z 195.088 minus the mass of the proton (1.0078), or 194.080. Caffeine has the elemental composition C₈H₁₀N₄O₂, so the molecular weight of caffeine is 194.080, which matches what we measured.

If we only have a low-resolution mass spectrometer (such as a quadrupole MS), we will only be able to measure the molecular weight to about one decimal place, but the JEOL AccuTOF-DART measures accurate masses with errors in the 3^rd or 4^th decimal place. Accurate molecular weight determination is important information for synthetic chemists.

If we want to identify an unknown compound, the molecular weight is useful information, but not enough to uniquely identify a molecule. Knowing the accurate mass is considerably more selective than just having an integer mass. If we search the NIST 20 mass spectral database for compounds with an integer molecular weight of 194, we find 1277 compounds. Limiting the search to 194.080 with an error tolerance of +/- 0.001 u returns 37 compounds.

Fortunately, an accurate-mass system like the AccuTOF-DART with DART-MS provides more information than just the molecular weight. In the next few articles, we’ll see how to determine the elemental composition from accurate-mass DART-MS data.

DART-MS can be used to determine the molecular weight of molecules. To learn more about JEOL mass spectrometers and the AccuTOF-DART system, please visit us here.

How helium DART-MS forms positive ions

Wed, 05 Apr 2023 15:01:57 GMT

In this post, I explain, step-by-step how ambient ionization with DART-MS forms positive ions by reactions of excited-state helium with atmospheric water.

Penning ionization

The first step in DART-MS involves the transfer of energy from highly energetic excited-state atoms to neutral molecules to form a positive ion and an electron. This is called Penning ionization after a short article published by F. W. Penning in 1927. A simplified DART-MS mechanism is represented in the following reaction:

M^* refers to a long-lived excited-state (“Metastable”) atom, H₂O denotes a water molecule, H₂O^+• denotes a positively charged water ion and e^— denotes an electron with its negative charge. The exact mechanism may be more complex -- for example, nitrogen in the air may play a role in reactions that ionize water molecules. In any case, we can see the result of the next step.

Charged water clusters

The water ions formed in the previous step react with neutral water molecules to produce hydronium ions (H₃O⁺) and protonated water clusters [(H₂O)n + H]^+•.

Protonated water clusters and trace background ions in positive-ion DART

The sample is ionized

In the last step, the protonated water clusters transfer a proton to the sample:

This will happen if the sample must have a higher proton affinity than water. This is generally true for basic molecules (for example, drugs like caffeine and cocaine) and for many samples with a heteroatom (O, S, N, P) or site of unsaturation (multiple bonds). This reaction won’t happen for very nonpolar molecules (for example, saturated hydrocarbons) and it isn’t the most favorable reaction for molecules like carboxylic acids and phenols. The figure below shows an AccuTOF-DART positive-ion mass spectrum from the NIST DART Forensic Database for caffeine.

Positive-ion DART mass spectrum of caffeine measured on the JEOL AccuTOF-DART

The simplest mechanism for forming positive ions with DART involves reactions of charged water clusters with the sample to produce a protonated molecule [S + H]⁺. In future posts, I’ll describe other reactions that can happen, but the next series of articles will discuss the information we can obtain from the accurate-mass data and isotope information in the DART-MS positive-ion mass spectrum. To learn more about JEOL mass spectrometers and the AccuTOF-DART system, please visit us here.