Mass spectrometry (MS) has become the central technique that is extensively used for the analysis of molecular structures of unknown compounds in the gas phase. It manipulates the molecules by converting them into ions using various ionization sources. With high-resolution MS, accurate molecular weights (MW) of the intact molecular ions can be measured so that they can be assigned a molecular formula with high confidence. Furthermore, the application of tandem MS has enabled detailed structural characterization by breaking the intact molecular ions and protonated or deprotonated molecules into key fragment ions. This approach is not only used for the structural elucidation of small molecules (MW < 2000 Da), but also crucial biopolymers such as proteins and polypeptides; therefore, MS has been extensively used in multiomics studies for revealing the structures and functions of important biomolecules and their interactions with each other. The high sensitivity of MS has enabled the analysis of low-level analytes in complex matrices. It is also a versatile technique that can be coupled with separation techniques, including chromatography and ion mobility, and many other analytical instruments such as NMR. In this review, we aim to focus on the technical advances of MS-based structural elucidation methods over the past five years, and provide an overview of their applications in complex mixture analysis. We hope this review can be of interest for a wide range of audiences who may not have extensive experience in MS-based techniques.

Alkanes and [B₁₂X₁₂]²⁻ (X = Cl, Br) are both stable compounds which are difficult to functionalize. Here we demonstrate the formation of a boron−carbon bond between these substances in a two-step process. Fragmentation of [B₁₂X₁₂]²⁻ in the gas phase generates highly reactive [B₁₂X₁₁]⁻ ions which spontaneously react with alkanes. The reaction mechanism was investigated using tandem mass spectrometry and gas-phase vibrational spectroscopy combined with electronic structure calculations. [B₁₂X₁₁]⁻ reacts by an electrophilic substitution of a proton in an alkane resulting in a B−C bond formation. The product is a dianionic [B₁₂X₁₁C_nH_2n+1]²⁻ species, to which H⁺ is electrostatically bound. High-flux ion soft landing was performed to codeposit [B₁₂X₁₁]⁻ and complex organic molecules (phthalates) in thin layers on surfaces. Molecular structure analysis of the product films revealed that C−H functionalization by [B₁₂X₁₁]⁻ occurred in the presence of other more reactive functional groups. This observation demonstrates the utility of highly reactive fragment ions for selective bond formation processes and may pave the way for the use of gas-phase ion chemistry for the generation of complex molecular structures in the condensed phase. Significance Functionalization of unreactive molecules is a significant chemical challenge relevant to the conversion of abundant feedstocks such as alkanes into high-value chemicals. Herein, we demonstrate a new mechanism of alkane functionalization by the substitution of a proton by an anion in an alkyl chain. The reactive anion used for this reaction is generated from a highly stable precursor. The reaction mechanism is established using experimental and computational approaches, and the products are collected in the condensed phase using high-flux mass-selected ion deposition. This paves the way for exploiting the properties of gaseous ions for the generation of complex molecular structures in the condensed phase.

The dismally low survival rate of ovarian cancer patients diagnosed with high-grade serous carcinoma (HGSC) emphasizes the lack of effective screening strategies. One major obstacle is the limited knowledge of the underlying mechanisms of HGSC pathogenesis at very early stages. Here, we present the first 10-month time-resolved serum metabolic profile of a triple mutant (TKO) HGSC mouse model, along with the spatial lipidome profile of its entire reproductive system. A high-coverage liquid chromatography mass spectrometry-based metabolomics approach was applied to longitudinally collected serum samples from both TKO (n = 15) and TKO control mice (n = 15), tracking metabolome and lipidome changes from premalignant stages to tumor initiation, early stages, and advanced stages until mouse death. Time-resolved analysis showed specific temporal trends for 17 lipid classes, amino acids, and TCA cycle metabolites, associated with HGSC progression. Spatial lipid distributions within the reproductive system were also mapped via ultrahigh-resolution matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and compared with serum lipid profiles for various lipid classes. Altogether, our results show that the remodeling of lipid and fatty acid metabolism, amino acid biosynthesis, TCA cycle and ovarian steroidogenesis are critical components of HGSC onset and development. These metabolic alterations are accompanied by changes in energy metabolism, mitochondrial and peroxisomal function, redox homeostasis, and inflammatory response, collectively supporting tumorigenesis.