The isotopic distribution conundrum

Although access to high-resolution mass spectrometry (MS), especially in the field of biomolecular MS, is becoming readily available due to recent advances in MS technology, the accompanied information on isotopic distribution in high-resolution spectra is not used at its full potential, mainly because of lack of knowledge and/or awareness. In this review, we give an insight into the practical problems related to calculating the isotopic distribution for large biomolecules, and present an overview of methods for the calculation of the isotopic distribution. We discuss the key events that triggered the development of various algorithms and explain the rationale of how and why the various isotopic-distribution calculations were performed. The review is focused around the developmental stages as briefly outlined below, starting with the first observation of an isotopic distribution. The observations of Beynon in the field of organic MS that chlorine appeared in a mass spectrum as two variants with odds 3:1 lie at the basis of the first wave of algorithms for the calculation of the isotopic distribution, based on the atomic composition of a molecule. From here on, we explain why more complex biomolecules such as peptides exhibit a highly complex isotope pattern when assayed by MS, and we discuss how combinatorial difficulties complicate the calculation of the isotopic distribution on computers. For this purpose, we highlight three methods, which were introduced in the 1980s. These are the stepwise procedure introduced by Kubinyi, the polynomial expansion from Brownawell and Fillippo, and the multinomial expansion from Yergey. The next development was instigated by Rockwood, who suggested to decompose the isotopic distribution in terms of their nucleon count instead of the exact mass. In this respect, we could claim that the term "aggregated" isotopic distribution is more appropriate. Due to the simplification of the isotopic distribution to its aggregated counterpart, Rockwood was able to use the convolution for the calculation of the "aggregated" isotopic distribution. Convolution methods are computationally efficient and economic in their memory usage. We spend a section on the work introduced by Rockwood during the 1990s. Due to recent breakthroughs in mass spectrometric technology and the widespread high-resolution instruments (e.g., FTICR-MS, FTOrbitrap-MS, and TOF-MS) that provide high-resolution, isotope-resolved, accurate mass data, there is an emerging need for algorithms that can calculate isotopic distributions for large biomolecules. The number of recent publications on this topic does witness this trend. The new methods are mostly based on complex mathematical developments such as, for example, cellular automata (Meija and Caruso [2004]. J Am Soc Mass Spectrom, 15(5):654-658), dynamic programming (Snider [2007]. J Am Soc Mass Spectrom, 18:1511-1515), and hierarchical models (Li et al. [2008] J Am Soc Mass Spectrom, 19:1867-1874). We also comment on the ideas to use Punnet squares and Pascal's triangle to introduce the concept of the isotopic distribution for educational and didactic purposes.     

Applications and advancements of FT-ICR-MS for interactome studies

The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MSⁿ experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.     

Issues and opportunities in accelerator mass spectrometry for stable isotopes

Accelerator mass spectrometry (AMS) has developed in the last 30 years many notable applications to the spectrometry of radioisotopes, particularly in radiocarbon dating. The instrumentation science of trace element AMS (TEAMS) that analyzes stable isotopes, also called Accelerator SIMS or MegaSIMS, while unique in many features, has also shared in many of these significant advances and has pushed TEAMS sensitivity to concentration levels surpassing many competing mass spectroscopic technologies. This review examines recent instrumentation developments, the capabilities of the new instrumentation and discernable trends for future development.     

Analysis of environmental organic matters by Ultrahigh-Resolution mass spectrometry—A review on the development of analytical methods

Owing to the increasing environmental and climate changes globally, there is an increasing interest in the molecular-level understanding of environmental organic compound mixtures, that is, the pursuit of complete and detailed knowledge of the chemical compositions and related chemical reactions. Environmental organic molecule mixtures, including those in air, soil, rivers, and oceans, have extremely complex and heterogeneous chemical compositions. For their analyses, ultrahigh-resolution and sub-ppb level mass accuracy, achievable using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are important. FT-ICR MS has been successfully used to analyze complex environmental organic molecule mixtures such as natural, soil, particulate, and dissolved organic matter. Despite its success, many limitations still need to be overcome. Sample preparation, ionization, structural identification, chromatographic separation, and data interpretation are some key areas that have been the focus of numerous studies. This review describes key developments in analytical techniques in these areas to aid researchers seeking to start or continue investigations for the molecular-level understanding of environmental organic compound mixtures.     

The development and application of matrix assisted laser desorption electrospray ionization: The teenage years

In the past 15 years, ambient ionization techniques have witnessed a significant incursion into the field of mass spectrometry imaging, demonstrating their ability to provide complementary information to matrix-assisted laser desorption ionization. Matrix-assisted laser desorption electrospray ionization is one such technique that has evolved since its first demonstrations with ultraviolet lasers coupled to Fourier transform-ion cyclotron resonance mass spectrometers to extensive use with infrared lasers coupled to orbitrap-based mass spectrometers. Concurrently, there have been transformative developments of this imaging platform due to the high level of control the principal group has retained over the laser technology, data acquisition software (RastirX), instrument communication, and image processing software (MSiReader). This review will discuss the developments of MALDESI since its first laboratory demonstration in 2005 to the most recent advances in 2021.     

Accurate and precise determination of isotopic ratios by MC‐ICP‐MS: A review

For many decades the accurate and precise determination of isotope ratios has remained a very strong interest to many researchers due to its important applications in earth, environmental, biological, archeological, and medical sciences. Traditionally, thermal ionization mass spectrometry (TIMS) has been the technique of choice for achieving the highest accuracy and precision. However, recent developments in multi‐collector inductively coupled plasma mass spectrometry (MC‐ICP‐MS) have brought a new dimension to this field. In addition to its simple and robust sample introduction, high sample throughput, and high mass resolution, the flat‐topped peaks generated by this technique provide for accurate and precise determination of isotope ratios with precision reaching 0.001%, comparable to that achieved with TIMS. These features, in combination with the ability of the ICP source to ionize nearly all elements in the periodic table, have resulted in an increased use of MC‐ICP‐MS for such measurements in various sample matrices. To determine accurate and precise isotope ratios with MC‐ICP‐MS, utmost care must be exercised during sample preparation, optimization of the instrument, and mass bias corrections. Unfortunately, there are inconsistencies and errors evident in many MC‐ICP‐MS publications, including errors in mass bias correction models. This review examines “state‐of‐the‐art” methodologies presented in the literature for achievement of precise and accurate determinations of isotope ratios by MC‐ICP‐MS. Some general rules for such accurate and precise measurements are suggested, and calculations of combined uncertainty of the data using a few common mass bias correction models are outlined. © 2009 Crown in the right of Canada. Published by Wiley Periodicals, Inc., Mass Spec Rev 28:990–1011, 2009     

基于高分辨质谱的代谢组学分析技术研究进展

代谢组学研究的目标是对生物体系中所有内源小分子代谢物进行全面的定性和定量表征.由于代谢物组成复杂、种类繁多、理化性质各异、且浓度差异大,给分析工作带来了极大的挑战.高分辨质谱因具有高灵敏度、高质量分辨率和质量精度、宽动态范围等优势,已成为代谢组学研究的主流分析工具.本文综述了近5年来基于高分辨质谱的代谢组学分析技术和方...     

Ion mobility spectrometry‐mass spectrometry (IMS‐MS) of small molecules: Separating and assigning structures to ions

The phenomenon of ion mobility (IM), the movement/transport of charged particles under the influence of an electric field, was first observed in the early 20th Century and harnessed later in ion mobility spectrometry (IMS). There have been rapid advances in instrumental design, experimental methods, and theory together with contributions from computational chemistry and gas‐phase ion chemistry, which have diversified the range of potential applications of contemporary IMS techniques. Whilst IMS‐mass spectrometry (IMS‐MS) has recently been recognized for having significant research/applied industrial potential and encompasses multi‐/cross‐disciplinary areas of science, the applications and impact from decades of research are only now beginning to be utilized for “small molecule” species. This review focuses on the application of IMS‐MS to “small molecule” species typically used in drug discovery (100–500 Da) including an assessment of the limitations and possibilities of the technique. Potential future developments in instrumental design, experimental methods, and applications are addressed. The typical application of IMS‐MS in relation to small molecules has been to separate species in fairly uniform molecular classes such as mixture analysis, including metabolites. Separation of similar species has historically been challenging using IMS as the resolving power, R, has been low (3–100) and the differences in collision cross‐sections that could be measured have been relatively small, so instrument and method development has often focused on increasing resolving power. However, IMS‐MS has a range of other potential applications that are examined in this review where it displays unique advantages, including: determination of small molecule structure from drift time, “small molecule” separation in achiral and chiral mixtures, improvement in selectivity, identification of carbohydrate isomers, metabonomics, and for understanding the size and shape of small molecules. This review provides a broad but selective overview of current literature, concentrating on IMS‐MS, not solely IMS, and small molecule applications. © 2012 Wiley Periodicals, Inc., Mass Spec Rev 32:43–71, 2013     

国产高分辨飞行时间质谱仪在药物分子结构鉴定中的应用

为了考察自主研发的API-TOF MS 10000电喷雾高分辨飞行时间质谱仪（ESI-TOF MS）对离子准确质量数测定的准确性及其在新药研发中的应用前景,采用该仪器对新药研发中涉及的291个天然产物及合成物进行质谱分析。以三氟乙酸钠为内标物进行仪器质量轴校准,将测试得到的目标离子准确质量数与理论准确质量数对比,计算两者的相对误差。结果表明：248个样品的分子质量测试结果与预期一致;对其中202个样品进行高分辨质谱测试,所得实验值与理论准确质量数之间的相对误差均小于5×10^-6;与预期不一致的实验结果提示样品的结构解析有误,并得到了其他波谱数据的验证。采用API-TOF MS 10000和美国AB Sciex公司的QSIAR Elite型Q/TOF MS对抗癌药物马来酸阿法替尼和降糖药利格列汀杂质进行质谱分析。结果表明,自主研发的API-TOF MS 10000与国际同类仪器对药物分子准确质量数的测试结果无明显差异,可以提供化合物准确的分子质量和分子式信息,是新药研发中药物分子结构解析的有力工具。     

Mass spectrometric characterization of naphthenic acids in environmental samples: a review

There is a growing need to develop mass spectrometric methods for the characterization of oil sands naphthenic acids (structural formulae described by C(n)H(2n+z)O(2) where n is the number of carbon atoms and "z" is referred to as the "hydrogen deficiency" and is equal to zero, or is a negative, even integer) present in environmental samples. This interest stems from the need to better understand their contribution to the total acid number of oil sands acids; along with assessing their toxicity in aquatic environments. Negative-ion electrospray ionization has emerged as the analytical technique of choice. For infusion samples, matrix effects are particularly evident for quantification in the presence of salts and co-elutants. However, such effects can be minimized for methods that employ chromatographic separation prior to mass spectrometry (MS) detection. There have been several advances for accurate identification of classes of naphthenic acid components that employ a range of MS hyphenated techniques. General trends measured for degradation of the NAs in the environment appear to be similar to those obtained with either low- or high-resolution MS. Future MS research will likely focus on (i) development of more reliable quantitative methods that use chromatography and internal standards, (ii) the utility of representative model naphthenic acids as surrogates for the complex NA mixtures, and (iii) development of congener-specific analysis of the principal toxic components.     

ICP‐MS‐Based strategies for protein quantification

In the post‐genomics era, proteomics has become a central branch in life sciences. An understanding of biological functions will not only rely on protein identification, but also on protein quantification in a living organism. Most of the existing methods for quantitative proteomics are based on isotope labeling combined with molecular mass spectrometry. Recently, a remarkable progress that utilizes inductively coupled plasma‐mass spectrometry (ICP‐MS) as an attractive complement to electrospray MS and MALDI MS for protein quantification, especially for absolute quantification, has been achieved. This review will selectively discuss the recent advances of ICP‐MS‐based technique, which will be expected to further mature and to become one of the key methods in quantitative proteomics. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 29:326–348, 2010     

Analysis of natural organic matter via fourier transform ion cyclotron resonance mass spectrometry: an overview of recent non-petroleum applications

Among the different techniques for mass analysis, ultra-high-resolution Fourier transform ion cyclotron resonance (FTICR) is the method of choice for highly complex samples, as it offers unrivaled mass accuracy and resolving power, combined with a high degree of flexibility in hybrid instruments as well as for ion activation techniques. FTICR instruments are readily embraced by the biological and biomedical research communities and applied over a wide range of applications for the analysis of biomolecules such as carbohydrates, lipids, nucleic acids, and proteins. In the field of natural organic matter (NOM) analysis, petroleum-related studies currently dominate FTICR-MS applications. Recently, however, there is a growing interest in developing high-performance MS methods for the characterization of NOM samples from natural aquatic and terrestrial environments. Here, we present an overview of FTICR-MS techniques for complex, non-petroleum NOM samples, including data analysis and novel tandem mass spectrometry (MS/MS) methods for structural classifications. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd.     

高温气冷堆及其乏燃料中核素的质谱分析技术

质谱技术发展初期主要用于与核工业相关的无机同位素丰度的测定,随着核工业的兴起与发展,质谱技术被广泛应用于核燃料与核材料中杂质分析、核燃料燃耗测定以及核素分析等领域。本工作从质谱技术用于高温气冷堆运行中产生的氚检测、乏燃料中痕量钚（Pu）和镎（Np）测定以及乏燃料中¹⁴C测定的原理及应用、研究方法的优缺点三方面展开论述,阐述了用于高温气冷堆及其乏燃料中核素分析方面的气体同位素质谱仪（GIMS）、电感耦合等离子体质谱仪（ICP-MS）、激光共振电离质谱仪（LRIMS）以及加速器质谱仪（AMS）的研制及应用现状,分析了仪器本身及其应用方面存在的问题及发展趋势,讨论了未来相关质谱技术的发展方向,并提出可能的解决方案。为了使质谱技术能够更加有效地应用于高温气冷堆的研究,迫切需要发展体积小、结构简单、便于操作的智能化仪器。     

THE PRESENT AND FUTURE OF THE MASS SPECTROMETRY-BASED INVESTIGATION OF THE EXOSOME LANDSCAPE

Exosomes are critical intercellular messengers released upon the fusion of multivesicular bodies with the cellular plasma membrane that deliver their cargo in the form of extracellular vesicles. Containing numerous nonrandomly packed functional proteins, lipids, and RNAs, exosomes are vital intercellular messengers that contribute to the physiologic processes of the healthy organism. During the post-genome era, exosome-oriented proteomics have garnered great interest. Since its establishment, mass spectrometry (MS) has been indispensable for the field of proteomics research and has advanced rapidly to interrogate biological samples at a higher resolution and sensitivity. Driven by new methodologies and more advanced instrumentation, MS-based approaches have revolutionized our understanding of protein biology. As the access to online proteomics database platforms has blossomed, experimental data processing occurs with more speed and accuracy. Here, we review recent advances in the technological progress of MS-based proteomics and several new detection strategies for MS-based proteomics research. We also summarize the use of integrated online databases for proteomics research in the era of big data. © 2020 John Wiley & Sons Ltd. Mass Spec Rev     

Tandem mass spectrometry in the study of fatty acids,bile acids,and steroids

Over the last 50 years, the mass spectrometry of lipids has evolved to become one of the most mature techniques in biomolecule analysis. Many volatile and non-polar lipids are directly amenable to analysis by gas-chromatography-mass spectrometry (GC-MS), a technique that combines the unsurpassed separation properties of gas-chromatography with the sensitivity and selectivity of electron ionization mass spectrometry. Less volatile and/or thermally labile lipids can be analyzed by GC-MS, following appropriate sample derivatization. However, many complex lipids are not readily analyzed by GC-MS, and it is these molecules that are the subject of the current review. Since the early 1970s, there have been three outstanding developments in mass spectrometry that are particularly appropriate in lipid analysis; i.e., the introduction of (i) fast atom bombardment (FAB); (ii) electrospray (ES); and (iii) tandem mass spectrometry (MS/MS). The FAB and ES ionization techniques will be discussed in relation to MS/MS, and examples of their application in biochemical studies will be presented. The review will concentrate on the analysis of fatty acids, bile acids, steroid conjugates, and neutral steroids.     

基于电喷雾质谱的反应监测研究进展

电喷雾质谱(ESI-MS)因具有灵敏度高、响应速度快、分辨率高、原位在线监测等特点,广泛应用于反应监测领域。本文主要从不同离子化技术角度,综述了电喷雾质谱在反应监测和机理研究方面的进展。重点介绍了在线电喷雾质谱技术,其中包括解吸附电喷雾离子化质谱（DESI-MS）、萃取电喷雾离子化质谱（EESI-MS）、纳升电喷雾离子化质谱（nESI-MS）、超声喷雾离子化质谱（SSI-MS）以及其他在线电喷雾离子化质谱在反应监测中的应用。最后,对电喷雾质谱在反应监测的发展趋势进行总结和展望。     

A History of Molecular Level Analysis of Natural Organic Matter by FTICR Mass Spectrometry and The Paradigm Shift in Organic Geochemistry

Natural organic matter (NOM) is a complex mixture of biogenic molecules resulting from the deposition and transformation of plant and animal matter. It has long been recognized that NOM plays an important role in many geological, geochemical, and environmental processes. Of particular concern is the fate of NOM in response to a warming climate in environments that have historically sequestered carbon (e.g., peatlands and swamps) but may transition to net carbon emitters. In this review, we will highlight developments in the application of high-field Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) in identifying the individual components of complex NOM mixtures, focusing primarily on the fraction that is dissolved in natural waters (dissolved organic matter or DOM). We will first provide some historical perspective on developments in FTICR technology that made molecular-level characterizations of DOM possible. A variety of applications of the technique will then be described, followed by our view of the future of high-field FTICR MS in carbon cycling research, including a particularly exciting metabolomic approach.     

高效液相色谱-高分辨质谱法研究药物代谢产物的数据处理策略

高效液相色谱-高分辨质谱（HPLC-HRMS）联用技术具有高灵敏度、快速和高质量准确度的特点,是药物代谢产物分析的有力手段。通过使用HPLC-HRMS产生高分辨质谱数据（高分辨质量数、多级质谱数据、同位素分布）,结合多重采集后数据处理技术,可用于药物代谢产物的快速发现和结构鉴定。本工作综述了近年来基于HPLC-HRMS技术应用最为广泛的几种数据挖掘策略及应用,如,提取离子色谱、质量亏损过滤、同位素过滤、本底扣除、产物离子过滤、质谱树状图过滤、SWATH和MS^E以及这些技术的联用等。通过合理地使用其中一种或几种策略对HPLC-HRMS产生的数据进行处理,可以有效地进行药物代谢产物的发现和鉴定。     

Mass spectrometry of atmospheric aerosols--recent developments and applications. Part I: Off-line mass spectrometry techniques

Many of the significant advances in our understanding of atmospheric particles can be attributed to the application of mass spectrometry. Mass spectrometry provides high sensitivity with a fast response time to probe chemically complex particles. This review focuses on recent developments and applications in the field of mass spectrometry of atmospheric aerosols. In Part I of this two-part review, we concentrate on off-line mass spectrometry techniques, which require sample collection on filters but can provide detailed molecular speciation. In particular, off-line mass spectrometry techniques utilizing tandem mass spectrometry experiments and high resolution mass analyzers provide improved insight into secondary organic aerosol formation and heterogeneous reaction pathways through detailed structural elucidation at the molecular level.     

Chemical derivatization strategy for mass spectrometry-based lipidomics

Lipids, serving as the structural components of cellular membranes, energy storage, and signaling molecules, play the essential and multiple roles in biological functions of mammals. Mass spectrometry (MS) is widely accepted as the first choice for lipid analysis, offering good performance in sensitivity, accuracy, and structural characterization. However, the untargeted qualitative profiling and absolute quantitation of lipids are still challenged by great structural diversity and high structural similarity. In recent decade, chemical derivatization mainly targeting carboxyl group and carbon-carbon double bond of lipids have been developed for lipidomic analysis with diverse advantages: (i) offering more characteristic structural information; (ii) improving the analytical performance, including chromatographic separation and MS sensitivity; (iii) providing one-to-one chemical isotope labeling internal standards based on the isotope derivatization regent in quantitative analysis. Moreover, the chemical derivatization strategy has shown great potential in combination with ion mobility mass spectrometry and ambient mass spectrometry. Herein, we summarized the current states and advances in chemical derivatization-assisted MS techniques for lipidomic analysis, and their strengths and challenges are also given. In summary, the chemical derivatization-based lipidomic approach has become a promising and reliable technique for the analysis of lipidome in complex biological samples.