Mass Spectrometry Instrumentation Research Articles

Data Acquisition and Intraoperative Tissue Analysis on a Mobile, Battery-Operated, Orbitrap Mass Spectrometer.

Mass spectrometry has been increasingly explored in intraoperative studies as a potential technology to help guide surgical decision making. Yet, intraoperative experiments using high-performance mass spectrometry instrumentation present a unique set of operational challenges. For example, standard operating rooms are often not equipped with the electrical requirements to power a commercial mass spectrometer and are not designed to accommodate their permanent installation. These obstacles can impact progress and patient enrollment in intraoperative clinical studies because implementation of MS instrumentation becomes limited to specific operating rooms that have the required electrical connections and space. To expand our intraoperative clinical studies using the MasSpec Pen technology, we explored the feasibility of transporting and acquiring data on Orbitrap mass spectrometers operating on battery power in hospital buildings. We evaluated the effect of instrument movement including acceleration and rotational speeds on signal stability and mass accuracy by acquiring data using direct infusion electrospray ionization. Data were acquired while rolling the systems in/out of operating rooms and while descending/ascending a freight elevator. Despite these movements and operating the instrument on battery power, the relative standard deviation of the total ion current was <5% and the magnitude of the mass error relative to the internal calibrant never exceeded 5.06 ppm. We further evaluated the feasibility of performing intraoperative MasSpec Pen analysis while operating the Orbitrap mass spectrometer on battery power during an ovarian cancer surgery. We observed that the rich and tissue-specific molecular profile commonly detected from ovarian tissues was conserved when running on battery power. Together, these results demonstrate that Orbitrap mass spectrometers can be operated and acquire data on battery power while in motion and in rotation without losses in signal stability or mass accuracy. Furthermore, Orbitrap mass spectrometers can be used in conjunction to the MasSpec Pen while on battery power for intraoperative tissue analysis.

Mass spectrometric analysis of Odonthobuthus Doriae scorpion venom and its non-neutralized fractions after interaction with commercial antivenom

It is believed that antivenoms play a crucial role in neutralizing venoms. However, uncontrolled clinical effects appear in patients stung by scorpions after the injection of antivenom. In this research, non-neutralized components of the venom of the Iranian scorpion Odonthobuthus doriae were analyzed after interacting with the commercial antivenom available in the market. The venom and antivenom interaction was performed, then centrifuged, and the supernatant was analyzed by high-performance liquid chromatography (HPLC). Two peaks of Odonthobuthus doriae venom were observed in the chromatogram of the supernatant. Two components were isolated by HPLC and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) instruments. Peptide sequencing was done by Liquid Chromatography Quadrupole Time-of-Flight Tandem Mass Spectrometry (LC-Q-TOF MS/MS). Results indicate that the components of scorpion venom mainly have a molecular weight below 10 kDa, consisting of toxic peptides that disrupt the function of sodium and potassium channels. The MALDI-TOF MS results show that two toxic peptides with molecular masses of 6941 Da and 6396 Da were not neutralized by the antivenom. According to the MS/MS sequencing data, the components have been related to peptides A0A5P8U2Q6_MESEU and A0A0U4FP89_ODODO, which belong to the sodium and potassium channels toxins family, respectively.

Towards elevated perfluorooctanoic acid (PFOA) enrichment in water: Sequential liquid-liquid extraction pretreatment for ion chromatography detection

The widespread detection of perfluorooctanoic acid (PFOA) in the environment has raised significant concerns. The standard PFOA analytical method relies on expensive solid-phase extraction (SPE) and liquid chromatography tandem mass spectrometry (LC-MS/MS) instruments, making routine use prohibitive. We herein proposed a cost-effective yet novel enrichment method for determining PFOA at ng L−1 level. This method entailed a two-step sample preparation process: firstly, PFOA was extracted and enriched using a forward-extraction under acidic conditions, followed by a backward-extraction and enrichment step utilizing alkaline water. The enriched samples were subsequently subjected to a common ion chromatography (IC). Results reveal that maintaining a forward-extraction pH below its pKa value (2.8) is essential, as protonated PFOA proves effective in enhancing the enrichment factor (EF). The challenge lied in driving PFOA from forward-extractant to aqueous backward-extractant due to the decreased hydrophobicity of deprotonated PFOA (log Kow2 = 1.0). In addition, we found that evaporating forward-extractant with alkaline backward-extractant (containing 5% methanol) reduced potential analytical uncertainties associated with PFOA evaporation and sorption. Under optimal conditions, the method achieved a detection limit of 9.2 ng L−1 and an impressive EF value of 719. Comparison with SPE-LC-MS/MS confirmed the proposed method as a promising alternative for PFOA determination. Although initially targeted for PFOA, the novel methodology is likely applicable to preconcentration of other poly-fluoroalkyl substances.

Rapid Determination of Taraxacum kok-saghyz Rubber Content Using a Pyrolyzer Hyphenated with a Miniaturized Mass Spectrometer

Taraxacum kok-saghyz (TKS), a rubber-producing plant with excellent potential, emerges as a viable substitute for rubber tree (Hevea brasiliensis). While natural rubber is a desirable material, conventional techniques for assessing rubber content have faced challenges in meeting practical production requirements. To address this issue, we have developed a pyrolysis–mass spectrometry (PY-MS) instrument for the quantitative evaluation of natural rubber (NR) content in rubber-producing plants. The derived standard curve equation, established for the detection of TKS dry weight through external standard calibration, demonstrates a correlation coefficient (R2) surpassing 0.99. The method exhibits commendable recovery rates (93.27–107.83%), relative standard deviations (RSD ≤ 3.93%), and a swift analysis time of merely 10 min per sample, thereby enabling accurate and efficient quantification of NR dry weight. Additionally, the PY-MS system we designed can be modified for vehicular use, enabling on-site, in situ analysis, and it provides substantial support for TKS breeding and propagation efforts. This approach possesses significant potential for extensive utilization in the assessment of rubber content in rubber-producing plants other than TKS. The integration of pyrolysis–mass spectrometry for the identification of polymers with high molecular weight offers a valuable pathway for the examination of diverse polymers.

Simultaneous and on-line detection of organic and heavy metal components in water using a novel nebulization-assisted injection plasma ionization triple quadruple mass spectrometry instrument

BackgroundThe global release of organic and heavy metal components into natural water bodies is a major concern for the environment and human health. The assessment of water quality relies on analyzing organic and heavy metal components qualitatively and quantitatively. Real-time identification of organic and metal components in water systems requires different analytical techniques due to varying measurement requirements. Thus, on-line detecting both organic compounds and heavy metals in ambient water systems simultaneously using a single instrumentation setup presents a significant challenge. ResultsIn this study, an analytical technique of nebulization-assisted injection plasma ionization mass spectrometry (NI-PIMS) was developed. This novel method enables the simultaneous detection of heavy metals and organic compounds in water system with high sensitivity, which has been demonstrated by the limit of quantification (LOQ) values below 1.0 μg/L for the three sterols (Enrofloxacin, ciprofloxacin, and clenbuterol) and three heavy metals (Pb, Ba, and Cd). Moreover, the method was successfully applied to rapidly analyze real water samples from urban and rural areas in China. The analytical results are available in less than 0.5 min, and only a few microliters of sample are required for each analysis. Significance and noveltyAs far as we know, this is the first report of on-line simultaneous analysis of organic compounds and heavy metals in a water system using a single mass spectrometry instrument. Compared to traditional methods, NI-PIMS demonstrates higher efficiency, sensitivity, no or lower sample preparation, and less sample consumption. The advancement and widespread use of this technology are expected to enhance the effectiveness of mass spectrometers, broaden the applications, and play an important role in complex sample analysis in fields such as atmospheric science, environmental science, and earth science.

Accurate Detection of G-Series Agent Simulants by Pseudo-Multiple Reaction Monitoring on Miniature LIT-MS.

Rapid and accurate on-site detection of chemical warfare agents (CWAs) could defend military and civilian populations against current and emerging chemical weapons. With the development of ambient ionization and linear ion trap technology, the rapid and accurate quantitative determination method of CWAs based on direct ionization and multistage mass spectrometry has attracted widespread attention. In this study, a microliter electrospray ionization-miniature linear ion trap mass spectrometry (LIT-MS) instrument was designed and constructed, and the effects of quadrupole enhanced dipole resonance excitation on the resolution and sensitivity were investigated; consequently, the parameters of CWAs detection were optimized. Based on the broad time-frequency ion excitation technology, accurate multiple reaction monitoring (MRM) quantitative analysis of DMMP (G-series agent simulants, m/z 125 → m/z 93) was obtained. The linear correlation coefficient in the concentration range of 1 to 20 μg/mL could reach 99.02%, and the relative standard deviations (RSD) of continuous repeatability, interday repeatability, and intraday repeatability were all less than 10%. The results showed that the accurate pseudo-MRM detection method based on miniature linear ion trap mass spectrometry for CWAs detection was feasible.

Wearable sampling of proteins from human exhaled aerosols for nano-liquid chromatography-tandem mass spectrometry analysis: A pilot study.

Human exhaled breath usually contains unique proteins that may provide clues to characterize individual physiological activities and many diseases. However, the concentration of exhaled proteins in exhaled breath is extremely low and usually does not reach the detection limits of all online breath mass spectrometry instruments. Therefore, developing a new breath sampler for collecting and characterizing exhaled proteins is important. In this study, a new mask-based wearable sampler was developed by fixing metal materials into the inner surface of the KN95 mask. Human exhaled proteins could be directly adsorbed onto the metal material while wearing the mask. After sampling, the collected proteins were eluted, digested, and identified using nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). The adsorption of exhaled proteins was evaluated, showing that modified gold foil is an effective material for collecting exhaled proteins. Various endogenous proteins were successfully identified from exhaled breath, many of which can be potential biomarkers for disease diagnosis. By coupling the newly developed mask sampler with nano-LC-MS/MS, human exhaled proteins were successfully collected and identified. Our results show that the mask sampler is wearable, simple, and convenient, and the method is noninvasive for investigating disease diagnosis and human health.

Tandem Mass Spectrometry across Platforms.

PubChem serves as a comprehensive repository, housing over 100 million unique chemical structures representing the breadth of our chemical knowledge across numerous fields including metabolism, pharmaceuticals, toxicology, cosmetics, agriculture, and many more. Rapid identification of these small molecules increasingly relies on electrospray ionization (ESI) paired with tandem mass spectrometry (MS/MS), particularly by comparison to genuine standard MS/MS data sets. Despite its widespread application, achieving consistency in MS/MS data across various analytical platforms remains an unaddressed concern. This study evaluated MS/MS data derived from one hundred molecular standards utilizing instruments from five manufacturers, inclusive of quadrupole time-of-flight (QTOF) and quadrupole orbitrap "exactive" (QE) mass spectrometers by Agilent (QTOF), Bruker (QTOF), SCIEX (QTOF), Waters (QTOF), and Thermo QE. We assessed fragment ion variations at multiple collisional energies (0, 10, 20, and 40 eV) using the cosine scoring algorithm for comparisons and the number of fragments observed. A parallel visual analysis of the MS/MS spectra across instruments was conducted, consistent with a standard procedure that is used to circumvent the still prevalent issue of mischaracterizations as shown for dimethyl sphingosine and C20 sphingosine. Our analysis revealed a notable consistency in MS/MS data and identifications, with fragment ions' m/z values exhibiting the highest concordance between instrument platforms at 20 eV, the other collisional energies (0, 10, and 40 eV) were significantly lower. While moving toward a standardized ESI MS/MS protocol is required for dependable molecular characterization, our results also underscore the continued importance of corroborating MS/MS data against standards to ensure accurate identifications. Our findings suggest that ESI MS/MS manufacturers, akin to the established norms for gas chromatography mass spectrometry instruments, should standardize the collision energy at 20 eV across different instrument platforms.

A study of the transient gas flow affected ion transmission in atmospheric pressure interfaces based on large eddy simulation for electrospray ionization mass spectrometry

Modern atmosphere pressure interface (API) enables high-efficiency coupling between mass analyzers in high vacuum and atmosphere ionization sources such as electrospray ionization (ESI) source. The transient gas flow entering API possesses strong compressibility and turbulent characteristics, which exerts a huge impact on ion transmission. However, the instantaneous nature and vortical morphology of the turbulence in API and its affection in ion transmission were hardly covered in the reported research. Here we conduct a transient turbulent flow-affected ion transmission evaluation for two typical APIs, the ion funnel and the S-lens, based on scale-resolving large eddy simulation and electro-hydrodynamical ion tracing simulation. In our simulation, the transient properties of the gas flow in the two APIs are illustrated and analyzed in-depth. After experimentally validated on a homemade ESI-TOF-MS platform, the results suggest that the ion funnel can achieve a higher droplet desolvation rate by introducing a unique droplet recirculation mechanism. Meanwhile, the less-dispersed gas flow in S-lens is beneficial in actuating ions axially. In conclusion, the application of the scale-resolving turbulence model helps us to understand the complicated fluid-ion interaction mechanism in APIs and is promising in the development of mass spectrometry instruments of higher performance.

Post-translational modifications of proteins in cardiovascular diseases examined by proteomic approaches.

Over 400 different types of post-translational modifications (PTMs) have been reported and over 200 various types of PTMs have been discovered using mass spectrometry (MS)-based proteomics. MS-based proteomics has proven to be a powerful method capable of global PTM mapping with the identification of modified proteins/peptides, the localization of PTM sites and PTM quantitation. PTMs play regulatory roles in protein functions, activities and interactions in various heart related diseases, such as ischemia/reperfusion injury, cardiomyopathy and heart failure. The recognition of PTMs that are specific to cardiovascular pathology and the clarification of the mechanisms underlying these PTMs at molecular levels are crucial for discovery of novel biomarkers and application in a clinical setting. With sensitive MS instrumentation and novel biostatistical methods for precise processing of the data, low-abundance PTMs can be successfully detected and the beneficial or unfavorable effects of specific PTMs on cardiac function can be determined. Moreover, computational proteomic strategies that can predict PTM sites based on MS data have gained an increasing interest and can contribute to characterization of PTM profiles in cardiovascular disorders. More recently, machine learning- and deep learning-based methods have been employed to predict the locations of PTMs and explore PTM crosstalk. In this review article, the types of PTMs are briefly overviewed, approaches for PTM identification/quantitation in MS-based proteomics are discussed and recently published proteomic studies on PTMs associated with cardiovascular diseases are included.

Role of Hydroperoxyl Radicals in Heterogeneous Oxidation of Oxygenated Organic Aerosols.

Heterogeneous oxidative aging of organic aerosols (OA) occurs ubiquitously in the atmosphere, initiated by oxidants, such as the hydroxyl radicals (•OH). Hydroperoxyl radicals (HO2•) are also an important oxidant in the troposphere, and its gas-phase chemistry has been well studied. However, the role of HO2• in heterogeneous OA oxidation remains elusive. Here, we carry out •OH-initiated heterogeneous oxidation of several OA model systems under different HO2• conditions in a flow tube reactor and characterize the molecular oxidation products using a suite of mass spectrometry instrumentation. By using hydrogen-deuterium exchange (HDX) with thermal desorption iodide-adduct chemical ionization mass spectrometry, we provide direct observation of organic hydroperoxide (ROOH) formation from heterogeneous HO2• and peroxy radicals (RO2•) reactions for the first time. The ROOH may contribute substantially to the oxidation products, varied with the parent OA chemical structure. Furthermore, by regulating RO2• reaction pathways, HO2• also greatly influence the overall composition of the oxidized OA. Last, we suggest that the RO2• + HO2• reactions readily occur at the OA particle interface rather than in the particle bulk. These findings provide new mechanistic insights into the heterogeneous OA oxidation chemistry and help fill the critical knowledge gap in understanding atmospheric OA oxidative aging.

Biomonitoring: Developing a Beehive Air Volatiles Profile as an Indicator of Environmental Contamination Using a Sustainable In-Field Technique

The wellbeing of the honey bee colonies and the health of humans are connected in numerous ways. Therefore, ensuring the wellbeing of bees is a crucial component of fostering sustainability and ecological harmony. The colony collapse disorder (CCD) phenomenon was first reported in 2006 when the majority of bee colonies in Europe died out, due to an increase in infections, contamination of hives with agrochemical pesticides, and persistent organic pollutants (POPs). Only 6 years after the emergence of CCD, more than 6.5 million premature deaths were reported, as a consequence of persistent human exposure to air pollution. The insect species such as the honey bee Apis mellifera L. and the air matrix inside the beehive can be used as tools in biomonitoring, instead of traditional monitoring methods. This may have advantages in terms of cost-effective bioindicators of the environmental health status, showing the ability to record spatial and temporal pollutant variations. In this study, we present the sustainable in-field usage of the portable membrane inlet mass spectrometry (MIMS) instrument for an instant and effective determination of the level of environmental pollution by analytical identification of hive atmosphere volatile organic compound (VOC) contaminants, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), monocyclic aromatic hydrocarbons (BTEX) compounds, and pesticides. The samples were taken from hives located in urbanized and rural regions, highlighting variations in contamination. The MIMS results were benchmarked against a conventional laboratory sampling technique, such as GC-MS.

Characterization of Regolith And Trace Economic Resources (CRATER): An Orbitrap-based laser desorption mass spectrometry instrument for in situ exploration of the Moon.

Characterization of Regolith And Trace Economic Resources (CRATER), an Orbitrap™-based laser desorption mass spectrometry instrument designed to conduct high-precision, spatially resolved analyses of planetary materials, is capable of answering outstanding science questions about the Moon's formation and the subsequent processes that have modified its (sub)surface. Here, we describe the baseline design of the CRATER flight model, which requires <20 000 cm3 volume, <10kg mass, and <60 W peak power. The analytical capabilities and performance metrics of a prototype that meets the full functionality of the flight model are demonstrated. The instrument comprises a high-power, solid-state, pulsed ultraviolet (213 nm) laser source to ablate the surface of the lunar sample, a custom ion optical interface to accelerate and collimate the ions produced at the ablation site, and an Orbitrap mass analyzer capable of discriminating competing isobars via ultrahigh mass resolution and high mass accuracy. The CRATER instrument can measure elemental and isotopic abundances and characterize the organic content of lunar surface samples, as well as identify economically valuable resources for future exploration. An engineering test unit of the flight model is currently in development to serve as a pathfinder for near-term mission opportunities.

Application of Weighted Gene Co-Expression Network Analysis to Metabolomic Data from an ApoA-I Knockout Mouse Model.

As the ability to collect profiling data in metabolomics increases substantially with the advances in Liquid Chromatography-Mass Spectrometry (LC-MS) instruments, it is urgent to develop new and powerful data analysis approaches to match the big data collected and to extract as much meaningful information as possible from tens of thousands of molecular features. Here, we applied weighted gene co-expression network analysis (WGCNA), an algorithm popularly used in microarray or RNA sequencing, to plasma metabolomic data and demonstrated several advantages of WGCNA over conventional statistical approaches such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). By using WGCNA, a large number of molecular features were clustered into a few modules to reduce the dimension of a dataset, the impact of phenotypic traits such as diet type and genotype on the plasma metabolome was evaluated quantitatively, and hub metabolites were found based on the network graph. Our work revealed that WGCNA is a very powerful tool to decipher, interpret, and visualize metabolomic datasets.

Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis.

Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise data quality and can damage the chromatography and MS instruments. However, researchers often discover contamination issues only after they acquire the data. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and cost-effective contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in the MS sample preparation workflow. Only 1 μL of the sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom-up proteomic methods regarding the effectiveness of removing detergent, peptide recovery, reproducibility, and proteome coverage. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. ContamSPOT can also provide a unique readout of sample cleanliness for developing new MS-based sample preparation methods in the future.

Perspective on SPME-MS: Green and high-performance methods for rapid screening

The direct coupling of solid-phase microextraction (SPME) with mass spectrometry (MS) offers rapid analysis with high sensitivity and low matrix effects by benefiting from the integration of sampling, high enrichment, and clean-up functions of SPME. Eliminating chromatographic separation reduces the amount of gas/solvent needed for analysis, while direct desorption in SPME-MS consumes none or few microliters of organic solvents per sample, further enhancing the greenness of the SPME technology. Over the past two decades, the rapid evolution of SPME-MS has given rise to numerous novel technologies that employ diverse ionization techniques and interfaces, several of which have already been commercialized. Drawing from an extensive review published earlier this year and our research experience, we provide perspectives on three aspects of these technologies: interface design and automation, integration with state-of-art MS instrumentation, and anticipated future developments.

Prototyping an ionization source for non-engineers.

Novel mass spectrometry (MS) based analytical platforms have enabled scientists to detect and quantify molecules within biological and environmental samples more accurately. Novel MS instrumentation starts as a prototype and, after years of development, can become a commercial product to be used by the larger MS community. Without the initial prototype, many MS-based instruments today would not be produced. Additionally, biotechnology companies are the main drivers for research, development, and production of novel instruments, but the tools for prototyping instrumentation have never been more accessible. Here, we present a tutorial on prototyping instrumentation through the case study of developing the Next Generation IR-MALDESI source to show that an engineering degree is not required to design and construct a prototype instrument with modern hardware and software. We discuss the prototyping process, the necessary skills required for efficient prototyping, and information about common hardware and software used within initial prototypes.

Optimizing an airborne mass-balance methodology for accurate emission rate quantification of industrial facilities: A case study of industrial facilities in South Korea

Accurate estimation of emissions from industrial point sources is crucial in understanding the effectiveness of reduction efforts and establishing reliable emission inventories. In this study, we employ an airborne Chemical Ionization Mass Spectrometry (CIMS) instrument to quantify sulfur dioxide (SO2) emissions from prominent industrial facilities in South Korea, including power plants, a steel mill, and a petrochemical facility. Our analysis utilizes the box mass balance technique to derive SO2 emissions and associated uncertainty. We evaluate the interpolation methods between 2D kriging and 3D radial basis function. The results demonstrate that the total uncertainty of the box mass balance technique ranges from 5 % to 28 %, with an average of 20 %. Mixing ratio ground extrapolation from the lowest altitude of the airborne sampling to the ground emerges as the dominant source of uncertainty, followed by the determination of the boundary layer height. Adequate sampling at multiple altitudes is found to be essential in reducing the overall uncertainty by capturing the full extent of the plume. Furthermore, we assess the uncertainty of the single-height transect mass balance method commonly employed in previous studies. Our findings reveal an average precision of 47 % for this method, with the potential for overestimating emissions by up to 206 %. Samplings at fewer altitudes or with larger altitude gaps increase the risk of under-sampling and elevate method uncertainties. Therefore, this study provides a quantitative basis to evaluate previously airborne observational emission constraints.

Reproducibility in nontarget screening (NTS) of environmental emerging contaminants: Assessing different HLB SPE cartridges and instruments

Non-targeted screening (NTS) methods are integral in environmental research for detecting emerging contaminants. However, their efficacy can be influenced by variations in hydrophilic-lipophilic balance (HLB) solid phase extraction (SPE) cartridges and high-resolution mass spectrometry (HRMS) instruments across different laboratories. In this study, we scrutinized the influence of five HLB SPE cartridges (Nano, Weiqi, CNW, Waters, and J&K) and four LC-HRMS platforms (Agilent, Waters, Thermo, and AB SCIEX) on the identification of emerging environmental contaminants. Our results demonstrate that 87.6 % of the target compounds and over 59.6 % of the non-target features were consistently detected across all tested HLB cartridges, with an overall 71.2 % universally identified across the four LC-HRMS systems. Discrepancies in detection rates were primarily attributable to variations in retention time stability, mass stability of precursors and fragments, system cleanliness affecting fold change and p-values, and fragment response. These findings confirm the necessity of refining parameter criteria for NTS. Moreover, our study confirms the efficacy of the PyHRMS tool in analyzing and processing data from multiple instrumental platforms, reinforcing its utility for multi-platform NTS. Overall, our findings underscore the reliability and robustness of NTS methods in identifying potential water contaminants, while also highlighting factors that may influence these outcomes.

Recent Contributions of Mass Spectrometry-Based "Omics" in the Studies of Breast Cancer.

Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".