Journal of the American Society for Mass Spectrometry最新文献_第8页

Advancing the Prediction of MS/MS Spectra Using Machine Learning 利用机器学习推进 MS/MS 图谱预测工作

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c00154

Julia Nguyen, Richard Overstreet, Ethan King, Danielle Ciesielski

引用次数: 0

Advancing the Prediction of MS/MS Spectra Using Machine Learning 利用机器学习推进 MS/MS 图谱预测工作

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c0015410.1021/jasms.4c00154

Julia Nguyen, Richard Overstreet, Ethan King and Danielle Ciesielski*,

{"title":"Advancing the Prediction of MS/MS Spectra Using Machine Learning","authors":"Julia Nguyen, Richard Overstreet, Ethan King and Danielle Ciesielski*, ","doi":"10.1021/jasms.4c0015410.1021/jasms.4c00154","DOIUrl":"https://doi.org/10.1021/jasms.4c00154https://doi.org/10.1021/jasms.4c00154","url":null,"abstract":"Tandem mass spectrometry (MS/MS) is an important tool for the identification of small molecules and metabolites where resultant spectra are most commonly identified by matching them with spectra in MS/MS reference libraries. While popular, this strategy is limited by the contents of existing reference libraries. In response to this limitation, various methods are being developed for the in silico generation of spectra to augment existing libraries. Recently, machine learning and deep learning techniques have been applied to predict spectra with greater speed and accuracy. Here, we investigate the challenges these algorithms face in achieving fast and accurate predictions on a wide range of small molecules. The challenges are often amplified by the use of generic machine learning benchmarking tactics, which lead to misleading accuracy scores. Curating data sets, only predicting spectra for sufficiently high collision energies, and working more closely with experimental mass spectrometrists are recommended strategies to improve overall prediction accuracy in this nuanced field.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Achieving Electron Capture Dissociation in the Radio Frequency Linear Ion Trap without the Assistance of a Magnetic Field─A Simulation Study 在射频线性离子阱中实现无磁场辅助的电子俘获解离--一项模拟研究

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c0028710.1021/jasms.4c00287

Fuzhong Ni, Ziyang Song, Jianfeng Chen, Bingyin Xu, Fuxing Xu* and Li Ding*,

{"title":"Achieving Electron Capture Dissociation in the Radio Frequency Linear Ion Trap without the Assistance of a Magnetic Field─A Simulation Study","authors":"Fuzhong Ni, Ziyang Song, Jianfeng Chen, Bingyin Xu, Fuxing Xu* and Li Ding*, ","doi":"10.1021/jasms.4c0028710.1021/jasms.4c00287","DOIUrl":"https://doi.org/10.1021/jasms.4c00287https://doi.org/10.1021/jasms.4c00287","url":null,"abstract":"It is extremely difficult to inject a low-energy electron beam into a conventional radiofrequency (RF) linear ion trap for electron capture dissociation (ECD) without using a magnetic field to focus the electrons. In this study, the dynamic process of electrons in an RF field during their injection and transmission through a linear ion trap was simulated to determine the range of the RF phase where the electrons can be decelerated to meet the energy requirement for ECD. The ECD time window was expanded by applying a time-dependent compensation voltage to the cathode. The relationship between the cathode voltage and the phase of the RF voltage was determined. The ECD time window was increased to 49.4% of the total RF cycle after applying a compensation voltage. Between the phases of RF voltage of 0 and 0.975 π, at least 98.7% of electrons can be injected into the ECD reaction zone, and 94% of them had an energy less than 3 eV. The range of electron energy can also easily be shifted upward to enable hot electron capture dissociation.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rearrangement of Proline Complexes with Zn2+: An Infrared Multiple Photon Dissociation and Theoretical Investigation 脯氨酸与 Zn2+ 复合物的重排：红外多光子解离与理论研究

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c0032110.1021/jasms.4c00321

P. B. Armentrout*, Georgia C. Boles, Giel Berden and Jos Oomens,

{"title":"Rearrangement of Proline Complexes with Zn2+: An Infrared Multiple Photon Dissociation and Theoretical Investigation","authors":"P. B. Armentrout*, Georgia C. Boles, Giel Berden and Jos Oomens, ","doi":"10.1021/jasms.4c0032110.1021/jasms.4c00321","DOIUrl":"https://doi.org/10.1021/jasms.4c00321https://doi.org/10.1021/jasms.4c00321","url":null,"abstract":"Complexes of proline (Pro) cationized with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Complexes of intact Pro with CdCl+, CdCl+(Pro), a complex of (Zn+Pro-H)+ where a proton has been lost, as well as Zn+(Pro-H)(Pro) were formed by electrospray ionization. In order to identify the structures formed experimentally, the IRMPD spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for zinc complexes and B3LYP/def2-TZVP level with an effective core potential on cadmium for the CdCl+(Pro) system. For the latter complex, the main binding motif observed has a zwitterionic proline ligand structure, [CO2–]cc, where the metal binds to the two carboxylate oxygens. In contrast, for Zn+(Pro-H)(Pro), both ligands interact with zinc via a [N,CO–][N,CO] binding motif, where binding is observed at the carbonyl oxygens and nitrogens for both ligands, consistent with previous work. In both cases, contributions from different puckers of the proline ring may contribute. For (Zn+Pro-H)+, we identify that the structure is actually ZnH+(Pro-2H), in which the proline has been dehydrogenated and one of the hydrogens has migrated to form a covalent bond with Zn, which verifies a previous report relying on a single OH stretch band.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights 将 DIA 单细胞蛋白质组学数据与 DiagnoMass 蛋白质组学中枢整合以获得生物学洞察力

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c00187

Aline M. A. Martins, Marlon D. M. Santos, Amanda C. Camillo-Andrade, Aline Lima Leite, Janaina Sena Souza, Sandra Sánchez, Alysson R. Muotri, Paulo Costa Carvalho, John R. Yates III

{"title":"Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights","authors":"Aline M. A. Martins, Marlon D. M. Santos, Amanda C. Camillo-Andrade, Aline Lima Leite, Janaina Sena Souza, Sandra Sánchez, Alysson R. Muotri, Paulo Costa Carvalho, John R. Yates III","doi":"10.1021/jasms.4c00187","DOIUrl":"https://doi.org/10.1021/jasms.4c00187","url":null,"abstract":"Single-cell proteomics has emerged as a powerful technology for unraveling the complexities of cellular heterogeneity, enabling insights into individual cell functions and pathologies. One of the primary challenges in single-cell proteomics is data generation, where low mass spectral signals often preclude the triggering of MS2 events. This challenge is addressed by Data Independent Acquisition (DIA), a data acquisition strategy that does not depend on peptide ion isotopic signatures to generate an MS2 event. In this study, we present data generated from the integration of DIA single-cell proteomics with a version of the DiagnoMass Proteomic Hub that was adapted to handle DIA data. DiagnoMass employs a hierarchical clustering methodology that enables the identification of tandem mass spectral clusters that are discriminative of biological conditions, thereby reducing the reliance on search engine biases for identifications. Nevertheless, a search engine (in this work, DIA-NN) can be integrated with DiagnoMass for spectral annotation. We used single-cell proteomic data from iPSC-derived neuroprogenitor cell cultures as a test study of this integrated approach. We were able to differentiate between control and Rett Syndrome patient cells to discern the proteomic variances potentially contributing to the disease’s pathology. Our research confirms that the DiagnoMass-DIA synergy significantly enhances the identification of discriminative proteomic signatures, highlighting critical biological variations such as the presence of unique spectra that could be related to Rett Syndrome pathology.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rearrangement of Proline Complexes with Zn2+: An Infrared Multiple Photon Dissociation and Theoretical Investigation 脯氨酸与 Zn2+ 复合物的重排：红外多光子解离与理论研究

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c00321

P. B. Armentrout, Georgia C. Boles, Giel Berden, Jos Oomens

{"title":"Rearrangement of Proline Complexes with Zn2+: An Infrared Multiple Photon Dissociation and Theoretical Investigation","authors":"P. B. Armentrout, Georgia C. Boles, Giel Berden, Jos Oomens","doi":"10.1021/jasms.4c00321","DOIUrl":"https://doi.org/10.1021/jasms.4c00321","url":null,"abstract":"Complexes of proline (Pro) cationized with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Complexes of intact Pro with CdCl+, CdCl+(Pro), a complex of (Zn+Pro-H)+ where a proton has been lost, as well as Zn+(Pro-H)(Pro) were formed by electrospray ionization. In order to identify the structures formed experimentally, the IRMPD spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for zinc complexes and B3LYP/def2-TZVP level with an effective core potential on cadmium for the CdCl+(Pro) system. For the latter complex, the main binding motif observed has a zwitterionic proline ligand structure, [CO2–]cc, where the metal binds to the two carboxylate oxygens. In contrast, for Zn+(Pro-H)(Pro), both ligands interact with zinc via a [N,CO–][N,CO] binding motif, where binding is observed at the carbonyl oxygens and nitrogens for both ligands, consistent with previous work. In both cases, contributions from different puckers of the proline ring may contribute. For (Zn+Pro-H)+, we identify that the structure is actually ZnH+(Pro-2H), in which the proline has been dehydrogenated and one of the hydrogens has migrated to form a covalent bond with Zn, which verifies a previous report relying on a single OH stretch band.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights 将 DIA 单细胞蛋白质组学数据与 DiagnoMass 蛋白质组学中枢整合以获得生物学洞察力

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-11 DOI: 10.1021/jasms.4c0018710.1021/jasms.4c00187

Aline M. A. Martins, Marlon D. M. Santos, Amanda C. Camillo-Andrade, Aline Lima Leite, Janaina Sena Souza, Sandra Sánchez, Alysson R. Muotri, Paulo Costa Carvalho* and John R. Yates III*,

{"title":"Integrating DIA Single-Cell Proteomics Data with the DiagnoMass Proteomic Hub for Biological Insights","authors":"Aline M. A. Martins, Marlon D. M. Santos, Amanda C. Camillo-Andrade, Aline Lima Leite, Janaina Sena Souza, Sandra Sánchez, Alysson R. Muotri, Paulo Costa Carvalho* and John R. Yates III*, ","doi":"10.1021/jasms.4c0018710.1021/jasms.4c00187","DOIUrl":"https://doi.org/10.1021/jasms.4c00187https://doi.org/10.1021/jasms.4c00187","url":null,"abstract":"Single-cell proteomics has emerged as a powerful technology for unraveling the complexities of cellular heterogeneity, enabling insights into individual cell functions and pathologies. One of the primary challenges in single-cell proteomics is data generation, where low mass spectral signals often preclude the triggering of MS2 events. This challenge is addressed by Data Independent Acquisition (DIA), a data acquisition strategy that does not depend on peptide ion isotopic signatures to generate an MS2 event. In this study, we present data generated from the integration of DIA single-cell proteomics with a version of the DiagnoMass Proteomic Hub that was adapted to handle DIA data. DiagnoMass employs a hierarchical clustering methodology that enables the identification of tandem mass spectral clusters that are discriminative of biological conditions, thereby reducing the reliance on search engine biases for identifications. Nevertheless, a search engine (in this work, DIA-NN) can be integrated with DiagnoMass for spectral annotation. We used single-cell proteomic data from iPSC-derived neuroprogenitor cell cultures as a test study of this integrated approach. We were able to differentiate between control and Rett Syndrome patient cells to discern the proteomic variances potentially contributing to the disease’s pathology. Our research confirms that the DiagnoMass-DIA synergy significantly enhances the identification of discriminative proteomic signatures, highlighting critical biological variations such as the presence of unique spectra that could be related to Rett Syndrome pathology.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integration of Hydrogen–Deuterium Exchange Mass Spectrometry with Molecular Dynamics Simulations and Ensemble Reweighting Enables High Resolution Protein–Ligand Modeling 将氢氘交换质谱法与分子动力学模拟和集合重权重相结合，实现高分辨率蛋白质配体建模

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-10 DOI: 10.1021/jasms.4c00202

Kyle C. Kihn, Olivia Purdy, Vincent Lowe, Lenka Slachtova, Ally K. Smith, Paul Shapiro, Daniel J. Deredge

{"title":"Integration of Hydrogen–Deuterium Exchange Mass Spectrometry with Molecular Dynamics Simulations and Ensemble Reweighting Enables High Resolution Protein–Ligand Modeling","authors":"Kyle C. Kihn, Olivia Purdy, Vincent Lowe, Lenka Slachtova, Ally K. Smith, Paul Shapiro, Daniel J. Deredge","doi":"10.1021/jasms.4c00202","DOIUrl":"https://doi.org/10.1021/jasms.4c00202","url":null,"abstract":"Hydrogen–Deuterium exchange mass spectrometry’s (HDX-MS) utility in identifying and characterizing protein–small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein–ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen–Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein–small molecule ligand interactions. To that end, we employ a strategy combining computational protein–ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein–ligand pairs tested, the HDX derived protein–ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamics of the Aspiration of Charged Droplets into a LC-ESI-MS System 带电液滴吸入 LC-ESI-MS 系统的动力学原理

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-10 DOI: 10.1021/jasms.4c00238

Patricia Itzenhäuser, Ferdinand Max Wachter, Laura Lehmann, Michelle Rajkovic, Thorsten Benter, Walter Wißdorf

{"title":"Dynamics of the Aspiration of Charged Droplets into a LC-ESI-MS System","authors":"Patricia Itzenhäuser, Ferdinand Max Wachter, Laura Lehmann, Michelle Rajkovic, Thorsten Benter, Walter Wißdorf","doi":"10.1021/jasms.4c00238","DOIUrl":"https://doi.org/10.1021/jasms.4c00238","url":null,"abstract":"Electrospray ionization (ESI) enables coupling between liquid chromatography (LC) and mass spectrometry (MS). Since it is a gentle ionization method, it is frequently used for the analysis of large biomolecules. In recent years, several experimental setups have demonstrated that the use of ESI results in the formation of charged droplets that are aspirated into the vacuum systems of mass spectrometers. This results in a variety of consequences, such as instrument contamination, which can impede the analytical performance. We investigate the signatures of aspirated charged droplets with a commercial LC-ESI-MS system at analytical conditions. Previous observations without LC coupling are reproduced and show that significant droplet aspiration is probably taking place at analytical LC-ESI-MS conditions. This common phenomenon likely decreases the instrument sensitivity. Analyte can be released by isolation and fragmentation of droplet fragments; thus, aspirated droplets can mask analyte even in the mass analyzer region. The complex morphology of droplet MS/MS mass spectra is highly reproducible at the same experimental conditions. This implies the existence of distinct molecular reaction pathways of the droplet fragments. To assess the effect of droplet aspiration on analytical applications, relevant method and ion source parameters, which are commonly varied during method optimization, were investigated. Further variations of the solvent composition revealed that the aspirated droplets and their fragmentation are particularly sensitive to the solvent composition and thus also to the LC solvent gradient in an analytical experiment.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition 基于样品复用的靶向蛋白质组学增强型智能数据采集

IF 3.2 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2024-09-10 DOI: 10.1021/jasms.4c00234

Ka Yang, Joao A. Paulo, Steven P. Gygi, Qing Yu

{"title":"Enhanced Sample Multiplexing-Based Targeted Proteomics with Intelligent Data Acquisition","authors":"Ka Yang, Joao A. Paulo, Steven P. Gygi, Qing Yu","doi":"10.1021/jasms.4c00234","DOIUrl":"https://doi.org/10.1021/jasms.4c00234","url":null,"abstract":"Targeted proteomics has been playing an increasingly important role in hypothesis-driven protein research and clinical biomarker discovery. We previously created a workflow, Tomahto, to enable real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Coupled with the TMT 11-plex reagent, hundreds of proteins of interest from up to 11 samples can be targeted and accurately quantified in a single-shot experiment with remarkable sensitivity. However, room remains to further improve the sensitivity, accuracy, and throughput, especially for targeted studies demanding a high peptide-level success rate. Here, bearing in mind the goal to improve peptide-level targeting, we introduce several new functionalities in Tomahto, featuring the integration of gas-phase fractionation using the FAIMS device, an accompanying software program (TomahtoPrimer) to customize fragmentation for each peptide target, and support for higher multiplexing capacity with the latest TMTpro reagent. We demonstrate that adding these features to the Tomahto platform significantly improves overall success rate from 89% to 98% in a single 60 min targeted assay of 290 peptides across human cell lines, while boosting quantitative accuracy via reducing TMT reporter ion interference.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142221988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0