Sarah E. Bamford, Wil Gardner, David A Winkler, Benjamin W. Muir, Damminda Alahakoon and Paul J. Pigram*,
{"title":"Self-Organizing Maps for Secondary Ion Mass Spectrometry","authors":"Sarah E. Bamford, Wil Gardner, David A Winkler, Benjamin W. Muir, Damminda Alahakoon and Paul J. Pigram*, ","doi":"10.1021/jasms.4c0031810.1021/jasms.4c00318","DOIUrl":"https://doi.org/10.1021/jasms.4c00318https://doi.org/10.1021/jasms.4c00318","url":null,"abstract":"<p >Secondary ion mass spectrometry (SIMS) is a powerful analytical technique for characterizing the molecular and elemental composition of surfaces. Individual mass spectra can provide information about the mean surface composition, while spatial mapping can elucidate the spatial distributions of molecular species in 2D and 3D with no prior labeling of molecular targets. The data sets produced by SIMS techniques are large and inherently complex, often containing subtle relationships between spatial and molecular features. Machine learning algorithms are well suited to exploring this complexity, making them ideal for data analysis, interpretation, and visualization of SIMS data sets. One such algorithm, the self-organizing map (SOM), is particularly well suited to clustering similar samples and reducing the dimensionality of hyperspectral data sets. Here, we present an introduction to the SOM, a concise mathematical description, and recent examples of its use in SIMS and other related mass spectrometry techniques. These examples demonstrate how SOMs may be used to interpret high volumes of individual mass spectra, imaging, or depth profiling data sets. This review will be useful for specialists in SIMS and other mass spectral techniques seeking to explore self-organizing maps for data analysis.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142408130","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}
Carmen Llorens-Cebrià, Norberto Núñez-Seral, Yolanda Villena-Ortiz, Irene Martínez-Díaz, Maria José Soler, Roser Ferrer-Costa, Conxita Jacobs-Cachá, Joan López-Hellín
{"title":"Trypsin Partially Cleaves Apolipoprotein A-I (ApoA-I) Precursor into Mature ApoA-I Hindering the Quantification of Naturally Occurring ApoA-I Proteoforms by Liquid Chromatography in Multiple Reaction Monitoring Mode Mass Spectrometry (LC-MRM-MS)","authors":"Carmen Llorens-Cebrià, Norberto Núñez-Seral, Yolanda Villena-Ortiz, Irene Martínez-Díaz, Maria José Soler, Roser Ferrer-Costa, Conxita Jacobs-Cachá, Joan López-Hellín","doi":"10.1021/jasms.4c00155","DOIUrl":"https://doi.org/10.1021/jasms.4c00155","url":null,"abstract":"Apolipoprotein A-I (ApoA-I), one of the most abundant proteins in plasma and the major protein component of high-density lipoprotein (HDL), is naturally found in several proteoforms; two of them are ProApoA-I and mature ApoA-I. These two proteoforms of ApoA-I coexist in biological samples and differ only in their N-terminal end. Virtually, the only way to differentiate them is by detecting the proteoform-specific N-terminal proteolytic peptides (RHFWQQDEPPQSPWDR and DEPPQSPWDR, respectively) using liquid chromatography in multiple reaction monitoring mode mass spectrometry (LC-MRM-MS). We have developed a bottom-up LC-MRM-MS method to simultaneously detect proApoA-I and mature ApoA-I. To test the specificity of the method, we digested with trypsin purified mature ApoA-I and recombinant proApoA-I. As expected, only the N-term peptide corresponding to the mature ApoA-I proteoform (DEPPQSPWDR) was detected when digesting mature ApoA-I. However, the digestion of the proApoA-I produced not only the N-terminal peptide corresponding to proApoA-I (RHFWQQDEPPQSPWDR) but also the N-terminal tryptic peptide corresponding to mature ApoA-I (DEPPQSPWDR). This effect was produced by standard and high-specificity trypsin as well as by the Arg-C enzyme in a self-limited manner (approximately 10% of the total). The synthetic proApo-I peptide is not cleaved by trypsin, suggesting that the here reported effect is dependent on protein conformation. The effect is not negligible, as it can be detected by LC-MRM-MS, and correction calculations should be applied to accurately quantify proApoA-I and mature ApoA-I in biological samples where these two proteoforms may coexist.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257783","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}
Carmen Llorens-Cebrià, Norberto Núñez-Seral, Yolanda Villena-Ortiz, Irene Martínez-Díaz, Maria José Soler, Roser Ferrer-Costa*, Conxita Jacobs-Cachá* and Joan López-Hellín,
{"title":"Trypsin Partially Cleaves Apolipoprotein A-I (ApoA-I) Precursor into Mature ApoA-I Hindering the Quantification of Naturally Occurring ApoA-I Proteoforms by Liquid Chromatography in Multiple Reaction Monitoring Mode Mass Spectrometry (LC-MRM-MS)","authors":"Carmen Llorens-Cebrià, Norberto Núñez-Seral, Yolanda Villena-Ortiz, Irene Martínez-Díaz, Maria José Soler, Roser Ferrer-Costa*, Conxita Jacobs-Cachá* and Joan López-Hellín, ","doi":"10.1021/jasms.4c0015510.1021/jasms.4c00155","DOIUrl":"https://doi.org/10.1021/jasms.4c00155https://doi.org/10.1021/jasms.4c00155","url":null,"abstract":"<p >Apolipoprotein A-I (ApoA-I), one of the most abundant proteins in plasma and the major protein component of high-density lipoprotein (HDL), is naturally found in several proteoforms; two of them are ProApoA-I and mature ApoA-I. These two proteoforms of ApoA-I coexist in biological samples and differ only in their N-terminal end. Virtually, the only way to differentiate them is by detecting the proteoform-specific N-terminal proteolytic peptides (RHFWQQDEPPQSPWDR and DEPPQSPWDR, respectively) using liquid chromatography in multiple reaction monitoring mode mass spectrometry (LC-MRM-MS). We have developed a bottom-up LC-MRM-MS method to simultaneously detect proApoA-I and mature ApoA-I. To test the specificity of the method, we digested with trypsin purified mature ApoA-I and recombinant proApoA-I. As expected, only the N-term peptide corresponding to the mature ApoA-I proteoform (DEPPQSPWDR) was detected when digesting mature ApoA-I. However, the digestion of the proApoA-I produced not only the N-terminal peptide corresponding to proApoA-I (RHFWQQDEPPQSPWDR) but also the N-terminal tryptic peptide corresponding to mature ApoA-I (DEPPQSPWDR). This effect was produced by standard and high-specificity trypsin as well as by the Arg-C enzyme in a self-limited manner (approximately 10% of the total). The synthetic proApo-I peptide is not cleaved by trypsin, suggesting that the here reported effect is dependent on protein conformation. The effect is not negligible, as it can be detected by LC-MRM-MS, and correction calculations should be applied to accurately quantify proApoA-I and mature ApoA-I in biological samples where these two proteoforms may coexist.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00155","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142403729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chad R. Weisbrod*, Amy M. McKenna and Christopher L. Hendrickson,
{"title":"Selective Gas-Phase Depletion of Chemical Contaminants in Dissolved Organic Matter Increases Compositional Coverage by FT-ICR Mass Spectrometry","authors":"Chad R. Weisbrod*, Amy M. McKenna and Christopher L. Hendrickson, ","doi":"10.1021/jasms.4c0026110.1021/jasms.4c00261","DOIUrl":"https://doi.org/10.1021/jasms.4c00261https://doi.org/10.1021/jasms.4c00261","url":null,"abstract":"<p >Fourier transform ion cyclotron resonance mass spectrometry of dissolved organic matter (DOM) extracted from environmental samples provides molecular speciation that enables visualization of compositional trends in the fate and cycling of biogenic and anthropogenic organics. Often, chemical contamination is introduced during field sampling (i.e., remote locations, cannot use glass). Further, preconcentration of DOM by solid-phase extraction often results in chemical contamination. When chemical noise is a dominant fraction of the ion signal, mass spectral performance is degraded by reduction of the ion trap analyte accumulation capacity and enhanced ion cloud dephasing during ICR detection. We have developed gas-phase ion depletion of unwanted chemical contaminants during ion injection into the linear RF ion trap of the hybrid linear ion trap 21 T FT-ICR mass spectrometer that improves detection of analytes by removing unwanted chemical noise. We demonstrate improvements in signal-to-noise ratio, dynamic range, and the number of observed analytes in dissolved organic matter samples that results in a 40–100% increase in the number of identified analytes. In many cases, the number of peaks observed per nominal mass more than doubles over select <i>m</i>/<i>z</i> regions. This gas-phase “clean-up” can salvage precious samples challenged by sampling location, sample volume, or collection protocols that cannot be avoided and maximizes the compositional information obtained. Further, this approach is generalizable and extendable to any hybrid linear ion trap instrument platform (e.g., LTQ-Orbitrap or linear ion trap-TOF). We highlight the power of gas-phase depletion with electrospray ionization, but this method is also applicable to other ionization modes.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407947","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}
Maria Bochenek, Michał Aleksander Ciach, Sander Smeets, Omar Beckers, Jochen Vanderspikken, Błażej Miasojedow, Barbara Domżał, Dirk Valkenborg, Wouter Maes, Anna Gambin
{"title":"An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software","authors":"Maria Bochenek, Michał Aleksander Ciach, Sander Smeets, Omar Beckers, Jochen Vanderspikken, Błażej Miasojedow, Barbara Domżał, Dirk Valkenborg, Wouter Maes, Anna Gambin","doi":"10.1021/jasms.4c00225","DOIUrl":"https://doi.org/10.1021/jasms.4c00225","url":null,"abstract":"Conjugated organic polymers have substantial potential for multiple applications but their properties are strongly influenced by structural defects such as homocoupling of monomer units and unexpected end-groups. Detecting and/or quantifying these defects requires complex experimental techniques, which hinder the optimization of synthesis protocols and fundamental studies on the influence of structural defects. Mass spectrometry offers a simple way to detect these defects but a manual analysis of many complex spectra is tedious and provides only approximate results. In this work, we develop a computational methodology for analyzing complex mass spectra of organic copolymers. Our method annotates spectra similarly to a human expert and provides quantitative information about the proportions of signal assigned to each ion. Our method is based on the open-source Masserstein algorithm, which we modify to handle large libraries of reference spectra required for annotating complex mass spectra of polymers. We develop a statistical methodology to analyze the quantitative annotations and compare the statistical distributions of structural defects in polymer chains between samples. We apply this methodology to analyze commercial and lab-made samples of a benchmark polymer and show that the samples differ both in the amount and in the types of structural defects.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257782","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}
Maria Bochenek, Michał Aleksander Ciach, Sander Smeets, Omar Beckers, Jochen Vanderspikken, Błażej Miasojedow, Barbara Domżał, Dirk Valkenborg, Wouter Maes and Anna Gambin*,
{"title":"An Automated Analysis of Homocoupling Defects Using MALDI-MS and Open-Source Computer Software","authors":"Maria Bochenek, Michał Aleksander Ciach, Sander Smeets, Omar Beckers, Jochen Vanderspikken, Błażej Miasojedow, Barbara Domżał, Dirk Valkenborg, Wouter Maes and Anna Gambin*, ","doi":"10.1021/jasms.4c0022510.1021/jasms.4c00225","DOIUrl":"https://doi.org/10.1021/jasms.4c00225https://doi.org/10.1021/jasms.4c00225","url":null,"abstract":"<p >Conjugated organic polymers have substantial potential for multiple applications but their properties are strongly influenced by structural defects such as homocoupling of monomer units and unexpected end-groups. Detecting and/or quantifying these defects requires complex experimental techniques, which hinder the optimization of synthesis protocols and fundamental studies on the influence of structural defects. Mass spectrometry offers a simple way to detect these defects but a manual analysis of many complex spectra is tedious and provides only approximate results. In this work, we develop a computational methodology for analyzing complex mass spectra of organic copolymers. Our method annotates spectra similarly to a human expert and provides quantitative information about the proportions of signal assigned to each ion. Our method is based on the open-source Masserstein algorithm, which we modify to handle large libraries of reference spectra required for annotating complex mass spectra of polymers. We develop a statistical methodology to analyze the quantitative annotations and compare the statistical distributions of structural defects in polymer chains between samples. We apply this methodology to analyze commercial and lab-made samples of a benchmark polymer and show that the samples differ both in the amount and in the types of structural defects.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142403061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chad R. Weisbrod, Amy M. McKenna, Christopher L. Hendrickson
{"title":"Selective Gas-Phase Depletion of Chemical Contaminants in Dissolved Organic Matter Increases Compositional Coverage by FT-ICR Mass Spectrometry","authors":"Chad R. Weisbrod, Amy M. McKenna, Christopher L. Hendrickson","doi":"10.1021/jasms.4c00261","DOIUrl":"https://doi.org/10.1021/jasms.4c00261","url":null,"abstract":"Fourier transform ion cyclotron resonance mass spectrometry of dissolved organic matter (DOM) extracted from environmental samples provides molecular speciation that enables visualization of compositional trends in the fate and cycling of biogenic and anthropogenic organics. Often, chemical contamination is introduced during field sampling (i.e., remote locations, cannot use glass). Further, preconcentration of DOM by solid-phase extraction often results in chemical contamination. When chemical noise is a dominant fraction of the ion signal, mass spectral performance is degraded by reduction of the ion trap analyte accumulation capacity and enhanced ion cloud dephasing during ICR detection. We have developed gas-phase ion depletion of unwanted chemical contaminants during ion injection into the linear RF ion trap of the hybrid linear ion trap 21 T FT-ICR mass spectrometer that improves detection of analytes by removing unwanted chemical noise. We demonstrate improvements in signal-to-noise ratio, dynamic range, and the number of observed analytes in dissolved organic matter samples that results in a 40–100% increase in the number of identified analytes. In many cases, the number of peaks observed per nominal mass more than doubles over select <i>m</i>/<i>z</i> regions. This gas-phase “clean-up” can salvage precious samples challenged by sampling location, sample volume, or collection protocols that cannot be avoided and maximizes the compositional information obtained. Further, this approach is generalizable and extendable to any hybrid linear ion trap instrument platform (e.g., LTQ-Orbitrap or linear ion trap-TOF). We highlight the power of gas-phase depletion with electrospray ionization, but this method is also applicable to other ionization modes.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257798","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}
Jinfeng Ge, Yulin Qi, Sen Xu, Wenrui Yao, Jingyi Hou, Fu-Jun Yue, Dietrich A. Volmer, Pingqing Fu, Si-Liang Li
{"title":"Elucidating the Composition and Transformation of Dissolved Organic Matter at the Sediment–Water Interface Using High-Resolution Mass Spectrometry","authors":"Jinfeng Ge, Yulin Qi, Sen Xu, Wenrui Yao, Jingyi Hou, Fu-Jun Yue, Dietrich A. Volmer, Pingqing Fu, Si-Liang Li","doi":"10.1021/jasms.4c00223","DOIUrl":"https://doi.org/10.1021/jasms.4c00223","url":null,"abstract":"The exchange and transformation of dissolved organic matter (DOM) at the sediment–water interface are crucial factors in regulating watershed biogeochemistry, with the molecular composition of DOM serving as a pivotal determinant in elucidating this process. High-resolution mass spectrometry (HRMS) is an effective tool for resolving the composition of DOM. By analyzing the compositional characteristics of DOM at the sediment–water interface under three different salinities at the same latitude region in northern China, the findings indicate certain variations in component characteristics of DOM between low-salinity inland waters and high-salinity seawaters, with the former exhibiting greater molecular diversity and higher molecular weights, whereas the latter displayed a higher saturation and bioavailability. Notably, the presence of more CHOS substances in the low-salinity inland waters underscores the transformation of the DOM influenced by terrestrial inputs and anthropogenic activities. Conversely, the presence of more CHO and CHNO substances in high-salinity seawater underscores the microbial effects. The chemical transformation process from overlying water to pore water to sediments was characterized by methylation, hydrogenation, decarboxylation, and reduction, as determined by calculating the relations between the H/C and O/C ratios of different compound types. These findings indicate that HRMS can yield more refined results in revealing the process of DOM at the sediment–water interface under different environments, which provides a more reliable basis for a deeper understanding of the source–sink mechanism of sediment organic matter.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257784","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}
Jinfeng Ge, Yulin Qi*, Sen Xu, Wenrui Yao, Jingyi Hou, Fu-Jun Yue, Dietrich A. Volmer, Pingqing Fu and Si-Liang Li,
{"title":"Elucidating the Composition and Transformation of Dissolved Organic Matter at the Sediment–Water Interface Using High-Resolution Mass Spectrometry","authors":"Jinfeng Ge, Yulin Qi*, Sen Xu, Wenrui Yao, Jingyi Hou, Fu-Jun Yue, Dietrich A. Volmer, Pingqing Fu and Si-Liang Li, ","doi":"10.1021/jasms.4c0022310.1021/jasms.4c00223","DOIUrl":"https://doi.org/10.1021/jasms.4c00223https://doi.org/10.1021/jasms.4c00223","url":null,"abstract":"<p >The exchange and transformation of dissolved organic matter (DOM) at the sediment–water interface are crucial factors in regulating watershed biogeochemistry, with the molecular composition of DOM serving as a pivotal determinant in elucidating this process. High-resolution mass spectrometry (HRMS) is an effective tool for resolving the composition of DOM. By analyzing the compositional characteristics of DOM at the sediment–water interface under three different salinities at the same latitude region in northern China, the findings indicate certain variations in component characteristics of DOM between low-salinity inland waters and high-salinity seawaters, with the former exhibiting greater molecular diversity and higher molecular weights, whereas the latter displayed a higher saturation and bioavailability. Notably, the presence of more CHOS substances in the low-salinity inland waters underscores the transformation of the DOM influenced by terrestrial inputs and anthropogenic activities. Conversely, the presence of more CHO and CHNO substances in high-salinity seawater underscores the microbial effects. The chemical transformation process from overlying water to pore water to sediments was characterized by methylation, hydrogenation, decarboxylation, and reduction, as determined by calculating the relations between the H/C and O/C ratios of different compound types. These findings indicate that HRMS can yield more refined results in revealing the process of DOM at the sediment–water interface under different environments, which provides a more reliable basis for a deeper understanding of the source–sink mechanism of sediment organic matter.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407564","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}
{"title":"Investigation and Development of the BODIPY-Embedded Isotopic Signature for Chemoproteomics Labeling and Targeted Profiling","authors":"Rachel Joshi, Adam M. Hawkridge","doi":"10.1021/jasms.4c00246","DOIUrl":"https://doi.org/10.1021/jasms.4c00246","url":null,"abstract":"A common goal in mass spectrometry-based chemoproteomics is to directly measure the site of conjugation between the target protein and the small molecule ligand. However, these experiments are inherently challenging due to the low abundance of labeled proteins and the difficulty in identifying modification sites using standard proteomics software. Reporter tags that either generate signature fragment ions or isotopically encode target peptides can be used for the preemptive discovery of labeled peptides even in the absence of identification. We investigated the potential of BODIPY FL azide as a click chemistry enabled chemoproteomics reagent due to the presence of boron and the unique 1:4 natural abundance ratio of <sup>10</sup>B:<sup>11</sup>B. The isotopes of boron encode BODIPY-labeled peptides with a predictable pattern between the monoisotopic (M) and M+1 peaks. BODIPY-labeled peptides were identified in MS1 spectra using an R script that filters for the signature <sup>10</sup>B:<sup>11</sup>B intensity ratio and mass defect. Application of the boron detection script resulted in three times the labeled peptide coverage achieved for a BODIPY-conjugated BSA sample compared with untargeted data-dependent acquisition sequencing. Furthermore, we used the inherent HF neutral loss signature from BODIPY to assist with BODIPY-modified peptide identification. Finally, we demonstrate the application of this approach using the BODIPY-conjugated BSA sample spiked into a complex <i>E. coli</i>. digest. In summary, our results show that the commercially available BODIPY FL azide clicked to alkyne-labeled peptides provides a unique isotopic signature for pinpointing the site(s) of modification with the added potential for on- or off-line UV or fluorescence detection.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257797","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}