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Impact of Multipole Fields on the Performance and Dynamics of Quadrupole Linear Ion Traps.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-06 DOI: 10.1021/jasms.4c00488
Fulong Deng, Xingliang He, Hongen Sun, Bin Wu, Yixiang Duan, Zhongjun Zhao

Additional multipole fields are unavoidable in real quadrupole linear ion traps (QLITs) and play a crucial role in influencing their performance. In this study, the impact of these multipole fields on ion ejection and dynamics in QLITs is exhaustively analyzed using a vectorized Runge-Kutta method and a comprehensive theoretical model of ion vibration involving all the common multipole fields. The comparison of nonlinear resonance under different added multipole fields reveals obvious ion ejection from hexapole and octopole resonances as well as multiple resonance points in most multipole fields. Ion ejection with dipole excitation under these fields demonstrates distinct variations at different excitation working values, influenced by the inherent power distribution of ion motion in a linear quadrupole and the energy dispersion caused by the added multipole fields at varying stability parameters. Furthermore, theoretical and numerical analyses of ion dynamics mutually validate each other, offering the first comprehensive demonstration of ion excitation responses under various multipole fields across a wide stability range. The results show that for positive even-order multipole fields, forward scans lead to lower and more stable maximum amplitude responses compared to reverse scans, while the opposite is true for negative fields. In hexapole fields, the forward scan responses are lower than the reverse scan responses, and both increase sharply near nonlinear resonance points, regardless of field polarity. This work provides a thorough theoretical foundation for optimizing multipole field applications in QLITs.

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引用次数: 0
Computed Vibrational Heat Capacities for Gas-Phase Biomolecular Ions.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-06 DOI: 10.1021/jasms.5c00008
Lawren R Paris, Austin W Green, James S Prell

Collision induced dissociation (CID) and collision induced unfolding (CIU) experiments are important tools for determining the structures of and differences between biomolecular complexes with mass spectrometry. However, quantitative comparison of CID/CIU data acquired on different platforms or even using different regions of the same instrument can be very challenging due to differences in gas identity and pressure, electric fields, and other experimental parameters. In principle, these can be reconciled by a detailed understanding of how ions heat, cool, and dissociate or unfold in time as a function of these parameters. Fundamental information needed to model these processes for different ion types and masses is their heat capacity as a function of the internal (i.e., vibrational) temperature. Here, we use quantum computational theory to predict average heat capacities as a function of temperature for a variety of model biomolecule types from 100 to 3000 K. On a degree-of-freedom basis, these values are remarkably invariant within each biomolecule type and can be used to estimate heat capacities of much larger biomolecular ions. We also explore effects of ion heating, cooling, and internal energy distribution as a function of time using a home-built program (IonSPA). We observe that these internal energy distributions can be nearly Boltzmann for larger ions (greater than a few kDa) through most of the CID/CIU kinetic window after a brief (few-μs) induction period. These results should be useful in reconciling CID/CIU results across different instrument platforms and under different experimental conditions, as well as in designing instrumentation and experiments to control CID/CIU behavior.

碰撞诱导解离(CID)和碰撞诱导解折(CIU)实验是利用质谱确定生物分子复合物结构和差异的重要工具。然而,由于气体特性和压力、电场和其他实验参数的不同,定量比较在不同平台甚至同一仪器的不同区域获得的 CID/CIU 数据非常具有挑战性。原则上,只要详细了解离子如何随这些参数的变化而加热、冷却、解离或展开,就可以调和这些差异。为不同类型和质量的离子建立这些过程模型所需的基本信息是其热容量与内部(即振动)温度的函数关系。在这里,我们利用量子计算理论预测了 100 至 3000 K 范围内各种生物大分子模型的平均热容量与温度的函数关系。在自由度基础上,这些值在每种生物大分子类型中都具有显著的不变性,可用于估算更大生物大分子离子的热容量。我们还使用自建程序(IonSPA)探索了离子加热、冷却和内能分布随时间变化的影响。我们观察到,对于较大的离子(大于几 kDa)来说,经过短暂(几微秒)的诱导期后,这些内能分布在大部分 CID/CIU 动力学窗口中都可以接近玻尔兹曼。这些结果有助于协调不同仪器平台和不同实验条件下的 CID/CIU 结果,也有助于设计仪器和实验来控制 CID/CIU 行为。
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引用次数: 0
Navigating the Postdoc Experience.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-02-20 DOI: 10.1021/jasms.4c00448
Chae Kyung Jeon, Daniel D Vallejo, Michael T Marty

There are many reasons to consider postdoctoral research after completing a Ph.D. For those interested in academic careers at all levels, a postdoctoral research associate (PDRA) position is often required or at least preferred. Even for those interested in industry, government, or alternative careers, postdoctoral research provides opportunities to expand your knowledge and skill sets beyond your Ph.D. training. It can be a wonderful time to focus on research with minimal distractions and interruptions. However, there has been little discussion about the challenges of the postdoc transition. The postdoc experience can vary widely, but common challenges include transitioning into a new environment, learning new skills, serving in multiple roles as a mentor and mentee, different and sometimes unclear positions in the institution, and competition for limited opportunities. In this Commentary, we draw on our personal experiences and interviews with postdocs of various backgrounds and intersectionalities (gender, race, first-gen, neurodiversity, etc.) to discuss how to successfully navigate various aspects of the postdoc experience. Our perspective comes primarily within mass spectrometry (MS) research, but the interviews include several experiences outside of the MS field to develop discussions applicable to a broad range of PDRA experiences.

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引用次数: 0
The 34th Sanibel Conference on Mass Spectrometry: Mass Spectrometry in Energy and the Environment
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 DOI: 10.1021/jasms.5c0003510.1021/jasms.5c00035
Amy M. McKenna,  and , Janne Jänis, 
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引用次数: 0
Remembrance: Dr. Jean H. Futrell.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-01-30 DOI: 10.1021/jasms.4c00479
Richard D Smith, David W Koppenaal
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引用次数: 0
Structural Characterization of Dimeric Perfluoroalkyl Carboxylic Acid Using Experimental and Theoretical Ion Mobility Spectrometry Analyses.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 DOI: 10.1021/jasms.5c00007
Aurore L Schneiders, Johann Far, Lidia Belova, Allison Fry, Adrian Covaci, Erin S Baker, Edwin De Pauw, Gauthier Eppe

Per- and polyfluoroalkyl substances (PFAS) are contaminants of increasing concern, with over seven million compounds currently inventoried in the PubChem PFAS Tree. Recently, ion mobility spectrometry has been combined with liquid chromatography and high-resolution mass spectrometry (LC-IMS-HRMS) to assess PFAS. Interestingly, using negative electrospray ionization, perfluoroalkyl carboxylic acids (PFCAs) form homodimers ([2M-H]-), a phenomenon observed with trapped, traveling wave, and drift-tube IMS. In addition to the limited research on their effect on analytical performance, there is little information on the conformations these dimers can adopt. This study aimed to propose most probable conformations for PFCA dimers. Based on qualitative analysis of how collision cross section (CCS) values change with the mass-to-charge ratio (m/z) of PFCA ions, the PFCA dimers were hypothesized to likely adopt a V-shaped structure. To support this assumption, in silico geometry optimizations were performed to generate a set of conformers for each possible dimer. A CCS value was then calculated for each conformer using the trajectory method with Lennard-Jones and ion-quadrupole potentials. Among these conformers, at least one of the ten lowest-energy conformers identified for each dimer exhibited theoretical CCS values within a ±2% error margin compared to the experimental data, qualifying them as plausible structures for the dimers. Our findings revealed that the fluorinated alkyl chains in the dimers are close to each other due to a combination of C-F···O=C and C-F···F-C stabilizing interactions. These findings, together with supplementary investigations involving environmentally relevant cations, may offer valuable insights into the interactions and environmental behavior of PFAS.

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引用次数: 0
HRMS-Viewer: Software for High Resolution Mass Spectrometry Formula Assignment and Data Visualization.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-02-19 DOI: 10.1021/jasms.4c00442
Junyang Chen, Chen He, Jianxun Wu, Yahe Zhang, Quan Shi

Accurately assigning formulas to thousands of peaks generated by ultrahigh resolution mass spectrometry in a single analysis poses a significant challenge, especially when dealing with diverse molecular compositions across complex mixtures. This difficulty is further compounded by the lack of an established universal mass calibration and formula assignment method. We have developed HRMS-Viewer, a Python-based software tool designed for processing ultrahigh resolution mass spectrometry data specific to petroleum and natural organic matter (NOM). The software employs an efficient, experience-driven approach for small molecule formula assignment, offering a streamlined yet intuitive workflow. Key features include advanced noise reduction, automatic or manual recalibration, real-time visualization of formula assignment results, and options for manual correction. During the workflow, HRMS-Viewer enables the visualization and manual control of critical steps including noise reduction, recalibration, peak identification, and data review.

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引用次数: 0
PNGaseF-Generated N-Glycans Adduct onto Peptides in the Gas Phase.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-02-12 DOI: 10.1021/jasms.4c00431
Valentina Rangel-Angarita, Joann Chongsaritsinsuk, Keira E Mahoney, Lea M Kim, Ryan J Chen, Akua A Appah-Sampong, Isabella P Tran, Alexandra D Steigmeyer, Marie A Hollenhorst, Stacy A Malaker

Glycoproteomics has recently increased in popularity due to instrumental and methodological advances. That said, O-glycoproteomic analysis is still challenging for various reasons, including signal suppression, search algorithm limitations, and co-occupancy of N- and O-glycopeptides. To decrease sample complexity and simplify analysis, most O-glycoproteomic workflows include PNGaseF digestion, which is an endoglycosidase that removes most N-glycan structures. Here, we report that N-glycans released from PNGaseF digestion were identified during data acquisition and hampered detection of O-glycopeptides. Importantly, we noted instances where free glycans adducted to unmodified peptides in the gas phase and were misidentified by search algorithms as O-glycopeptides. We confirmed the presence of free glycans in other experiments performed in our laboratory, as well as from data generated by other groups. To overcome this limitation, we demonstrated that released N-glycans can be removed using a molecular weight cut off filter prior to (glyco)protease digestion, which improves O-glycoproteomic coverage.

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引用次数: 0
Rapid and Non-Targeted Qualitative and Quantitative Detection of miRNA in Complex Biological Samples Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with a 3-Aminoquinoline and 2',4',6'-Trihydroxyacetophenone Ionic Liquid Matrix.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-01-30 DOI: 10.1021/jasms.4c00369
Shiwen Zhou, Jiancong Liao, Kailin Jiang, Huiwen Wang, Yaqin Liu, Hangming Xiong, Ping Wang, Yuanjiang Pan, Hongru Feng

A novel ionic liquid MALDI matrix, 3-aminoquinoline/2',4',6'-trihydroxyacetophenone monohydrate (3-AQ/THAP), was developed for the rapid qualitative and quantitative detection of miRNA from biological samples. Compared to the traditional matrix 2,5-dihydroxybenzoic acid (DHB) and previously reported oligonucleotide-specific matrices, such as 3-aminopicolinic acid (3-APA), 3-hydroxypicolinic acid (3-HPA), and 6-aza-2-thiothymine (ATT), the 3-AQ/THAP matrix offers several advantages. It produces fewer alkali metal adduct peaks, exhibits higher sensitivity, and ensures better spot-to-spot repeatability. The 3-AQ/THAP matrix provides broader mass coverage and can effectively detect oligonucleotides ranging from 3-mer to 50-mer while delivering single-base resolution and sequence information. Additionally, it significantly reduces the "sweet spot" effect with an RSD of less than 7% over 36 single-spot analyses. For oligonucleotides ranging from 16-mer to 26-mer, the linear range extends from 0.4 μM to 40 μM per spot, with an R2 greater than 0.988. Finally, miRNA in human plasma, fetal equine serum, and fetal bovine serum was successfully identified both qualitatively and quantitatively using the 3-AQ/THAP matrix. This matrix demonstrated excellent practicability for the detection of multiple miRNAs in complex biological samples.

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引用次数: 0
Faces of Mass Spectrometry/Jose Navarrete-Perea.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-03-05 Epub Date: 2025-02-04 DOI: 10.1021/jasms.5c00020
Anne Brenner, J D Brookbank
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引用次数: 0
期刊
Journal of the American Society for Mass Spectrometry
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