Pub Date : 2016-11-23DOI: 10.5702/MASSSPECTROMETRY.S0052
Fumio Matsuda
Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10-100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism.
{"title":"Technical Challenges in Mass Spectrometry-Based Metabolomics.","authors":"Fumio Matsuda","doi":"10.5702/MASSSPECTROMETRY.S0052","DOIUrl":"https://doi.org/10.5702/MASSSPECTROMETRY.S0052","url":null,"abstract":"Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10-100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"8 1","pages":"S0052"},"PeriodicalIF":0.0,"publicationDate":"2016-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73298056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-23DOI: 10.5702/MASSSPECTROMETRY.S0053
Masamitsu Maekawa, K. Omura, Shoutaro Sekiguchi, T. Iida, D. Saigusa, Hiroaki Yamaguchi, N. Mano
In the urine of a Niemann-Pick disease type C (NPC) patient, we have identified three characteristic intense peaks that have not been observed in the urine of a 3β-hydroxysteroid-Δ5-C27-steroid dehydrogenase deficiency patient or a healthy infant and adult. Based on accurate masses of the protonated molecules, we focused on two of them as candidate NPC diagnostic markers. Two synthesized authentic preparations agreed with the two compounds found in NPC patient urine in regard to both chromatographic behavior and accurate masses of the deprotonated molecules. Moreover, the isotopic patterns of the deprotonated molecules, twin peaks unique to the sulfur-containing compounds appearing in their second isotope positions, and accurate masses of product ions observed at m/z 97 also agreed between the target compounds and authentic preparations. We identified the two compounds as the sulfated cholesterol metabolites as 3β-sulfooxy-7β-hydroxy-5-cholen-24-oic acid and 3β-sulfooxy-7-oxo-5-cholen-24-oic acid. These two compounds represent more promising candidate diagnostic markers for NPC diagnosis than three other candidates that are multiple conjugates of cholesterol metabolites, 3β-sulfooxy-7β-N-acetylglucosaminyl-5-cholen-24-oic acid and its glycine and taurine conjugates, although we have reported an analytical method for determining the urinary levels of these compounds using liquid chromatography/electrospray ionization tandem mass spectrometry, because of their lack of N-acetylglucosamine conjugation.
{"title":"Identification of Two Sulfated Cholesterol Metabolites Found in the Urine of a Patient with Niemann-Pick Disease Type C as Novel Candidate Diagnostic Markers.","authors":"Masamitsu Maekawa, K. Omura, Shoutaro Sekiguchi, T. Iida, D. Saigusa, Hiroaki Yamaguchi, N. Mano","doi":"10.5702/MASSSPECTROMETRY.S0053","DOIUrl":"https://doi.org/10.5702/MASSSPECTROMETRY.S0053","url":null,"abstract":"In the urine of a Niemann-Pick disease type C (NPC) patient, we have identified three characteristic intense peaks that have not been observed in the urine of a 3β-hydroxysteroid-Δ5-C27-steroid dehydrogenase deficiency patient or a healthy infant and adult. Based on accurate masses of the protonated molecules, we focused on two of them as candidate NPC diagnostic markers. Two synthesized authentic preparations agreed with the two compounds found in NPC patient urine in regard to both chromatographic behavior and accurate masses of the deprotonated molecules. Moreover, the isotopic patterns of the deprotonated molecules, twin peaks unique to the sulfur-containing compounds appearing in their second isotope positions, and accurate masses of product ions observed at m/z 97 also agreed between the target compounds and authentic preparations. We identified the two compounds as the sulfated cholesterol metabolites as 3β-sulfooxy-7β-hydroxy-5-cholen-24-oic acid and 3β-sulfooxy-7-oxo-5-cholen-24-oic acid. These two compounds represent more promising candidate diagnostic markers for NPC diagnosis than three other candidates that are multiple conjugates of cholesterol metabolites, 3β-sulfooxy-7β-N-acetylglucosaminyl-5-cholen-24-oic acid and its glycine and taurine conjugates, although we have reported an analytical method for determining the urinary levels of these compounds using liquid chromatography/electrospray ionization tandem mass spectrometry, because of their lack of N-acetylglucosamine conjugation.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"50 1","pages":"S0053"},"PeriodicalIF":0.0,"publicationDate":"2016-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87335769","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-23DOI: 10.5702/MASSSPECTROMETRY.A0051
Atsushi Kitanaka, M. Miyashita, A. Kubo, Takaya Satoh, M. Toyoda, H. Miyagawa
De novo sequencing is still essential in the identification of peptides and proteins from unexplored organisms whose sequence information is not available. One of the remaining problems in de novo sequencing is discrimination between Leu and Ile residues. The discrimination is possible based on differences in side chain fragmentation between Leu and Ile under high-energy collision-induced dissociation (HE-CID) conditions. However, this is observed only when basic residues, such as Arg and Lys, are present near the N- or C-terminal end. It has been shown that the charge derivatization at the N-terminal end by a quarternary ammonium or phosphonium moiety facilitates the side chain fragmentation by HE-CID. However, the effective backbone fragmentation by low-energy CID (LE-CID) is often hampered in those derivatives with a fixed charge. Previously, we demonstrated that the N-terminal charge derivatization with the structures having high proton affinity induced the preferential formation of b-ions under LE-CID conditions, allowing straightforward interpretation of product ion spectra. In the present study, we further investigated whether the same derivatization approach is also effective for discrimination between Leu and Ile under HE-CID conditions. Consequently, the side chain fragmentation of Leu and Ile residues was most effectively enhanced by the N-terminal derivatization with 4-(guanidinomethyl)benzoic acid among the tested structures. This derivatization approach, which is compatible with both HE- and LE-CID analysis, offers a straightforward and unambiguous de novo peptide sequencing method.
{"title":"N-Terminal Derivatization with Structures Having High Proton Affinity for Discrimination between Leu and Ile Residues in Peptides by High-Energy Collision-Induced Dissociation.","authors":"Atsushi Kitanaka, M. Miyashita, A. Kubo, Takaya Satoh, M. Toyoda, H. Miyagawa","doi":"10.5702/MASSSPECTROMETRY.A0051","DOIUrl":"https://doi.org/10.5702/MASSSPECTROMETRY.A0051","url":null,"abstract":"De novo sequencing is still essential in the identification of peptides and proteins from unexplored organisms whose sequence information is not available. One of the remaining problems in de novo sequencing is discrimination between Leu and Ile residues. The discrimination is possible based on differences in side chain fragmentation between Leu and Ile under high-energy collision-induced dissociation (HE-CID) conditions. However, this is observed only when basic residues, such as Arg and Lys, are present near the N- or C-terminal end. It has been shown that the charge derivatization at the N-terminal end by a quarternary ammonium or phosphonium moiety facilitates the side chain fragmentation by HE-CID. However, the effective backbone fragmentation by low-energy CID (LE-CID) is often hampered in those derivatives with a fixed charge. Previously, we demonstrated that the N-terminal charge derivatization with the structures having high proton affinity induced the preferential formation of b-ions under LE-CID conditions, allowing straightforward interpretation of product ion spectra. In the present study, we further investigated whether the same derivatization approach is also effective for discrimination between Leu and Ile under HE-CID conditions. Consequently, the side chain fragmentation of Leu and Ile residues was most effectively enhanced by the N-terminal derivatization with 4-(guanidinomethyl)benzoic acid among the tested structures. This derivatization approach, which is compatible with both HE- and LE-CID analysis, offers a straightforward and unambiguous de novo peptide sequencing method.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"39 1","pages":"A0051"},"PeriodicalIF":0.0,"publicationDate":"2016-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83734930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-10DOI: 10.5702/MASSSPECTROMETRY.A0049
Sayaka Nakamura, Hiroaki Sato, R. Tanaka, T. Yaguchi
We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus.
{"title":"Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification.","authors":"Sayaka Nakamura, Hiroaki Sato, R. Tanaka, T. Yaguchi","doi":"10.5702/MASSSPECTROMETRY.A0049","DOIUrl":"https://doi.org/10.5702/MASSSPECTROMETRY.A0049","url":null,"abstract":"We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"23 1","pages":"A0049"},"PeriodicalIF":0.0,"publicationDate":"2016-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80504893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-11-01DOI: 10.5702/MASSSPECTROMETRY.A0050
T. Fouquet, M. Torimura, Hiroaki Sato
The degradation routes of poly(vinyl pyrrolidone) (PVP) exposed to sodium hypochlorite (bleach) have been previously investigated using chemical analyses such as infrared spectroscopy. So far, no reports have proposed mass spectrometry (MS) as an alternative tool despite its capability to provide molecular and structural information using its single stage electrospray (ESI) or matrix assisted laser desorption ionization (MALDI) and multi stage (MS n ) configurations, respectively. The present study thus reports on the characterization of PVP after its exposure to bleach by high resolution MALDI spiralTOF-MS and Kendrick mass defect analysis providing clues as to the formation of a vinyl pyrrolidone/vinyl succinimide copolymeric degradation product. A thorough investigation of the fragmentation pathways of PVP adducted with sodium and proton allows one main route to be described-namely the release of the pyrrolidone pendant group in a charge remote and charge driven mechanism, respectively. Extrapolating this fragmentation pathway, the oxidation of vinyl pyrrolidone into vinyl succinimide hypothesized from the single stage MS is validated by the detection of an alternative succinimide neutral loss in lieu of the pyrrolidone release in the ESI-MS n spectra of the aged PVP sample. It constitutes an example of application of multi-stage mass spectrometry for the characterization of the degradation of polymeric samples at a molecular level.
{"title":"Multi-stage Mass Spectrometry of Poly(vinyl pyrrolidone) and Its Vinyl Succinimide Copolymer Formed upon Exposure to Sodium Hypochlorite.","authors":"T. Fouquet, M. Torimura, Hiroaki Sato","doi":"10.5702/MASSSPECTROMETRY.A0050","DOIUrl":"https://doi.org/10.5702/MASSSPECTROMETRY.A0050","url":null,"abstract":"The degradation routes of poly(vinyl pyrrolidone) (PVP) exposed to sodium hypochlorite (bleach) have been previously investigated using chemical analyses such as infrared spectroscopy. So far, no reports have proposed mass spectrometry (MS) as an alternative tool despite its capability to provide molecular and structural information using its single stage electrospray (ESI) or matrix assisted laser desorption ionization (MALDI) and multi stage (MS n ) configurations, respectively. The present study thus reports on the characterization of PVP after its exposure to bleach by high resolution MALDI spiralTOF-MS and Kendrick mass defect analysis providing clues as to the formation of a vinyl pyrrolidone/vinyl succinimide copolymeric degradation product. A thorough investigation of the fragmentation pathways of PVP adducted with sodium and proton allows one main route to be described-namely the release of the pyrrolidone pendant group in a charge remote and charge driven mechanism, respectively. Extrapolating this fragmentation pathway, the oxidation of vinyl pyrrolidone into vinyl succinimide hypothesized from the single stage MS is validated by the detection of an alternative succinimide neutral loss in lieu of the pyrrolidone release in the ESI-MS n spectra of the aged PVP sample. It constitutes an example of application of multi-stage mass spectrometry for the characterization of the degradation of polymeric samples at a molecular level.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"22 1","pages":"A0050"},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85822873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-09-02DOI: 10.5702/massspectrometry.S0051
T. Higashi, M. Yokota, Ayaka Goto, Kenji Komatsu, Takahiro Sugiura, Shoujiro Ogawa, M. Satoh, F. Nomura
A method for the simultaneous determination of 25-hydroxyvitamin D3 [25(OH)D3] and its 3-sulfate [25(OH)D3S] in newborn plasma, which is expected to be helpful in the assessment of the vitamin D status, using stable isotope-dilution liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) has been developed and validated. The plasma was pretreated based on the deproteinization and solid-phase extraction, then subjected to derivatization with 4-(4-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD). The derivatization enabled the accurate quantification of 25(OH)D3 without interference from 3-epi-25(OH)D3 and also facilitated the simultaneous determination of the two metabolites by LC/positive ESI-MS/MS. Quantification was based on the selected reaction monitoring with the characteristic fragmentation of the DAPTAD-derivatives during MS/MS. This method was reproducible (intra- and inter-assay relative standard deviations of 7.8% or lower for both metabolites) and accurate (analytical recovery, 95.4-105.6%). The limits of quantification were 1.0 ng/mL and 2.5 ng/mL for 25(OH)D3 and 25(OH)D3S, respectively, when using a 20-μL sample. The developed method was applied to the simultaneous determination of plasma 25(OH)D3 and 25(OH)D3S in newborns; it was recognized that the plasma concentration of 25(OH)D3S is significantly higher than that of 25(OH)D3, and preterm newborns have lower plasma 25(OH)D3S concentrations than full-term newborns.
{"title":"A Method for Simultaneous Determination of 25-Hydroxyvitamin D3 and Its 3-Sulfate in Newborn Plasma by LC/ESI-MS/MS after Derivatization with a Proton-Affinitive Cookson-Type Reagent.","authors":"T. Higashi, M. Yokota, Ayaka Goto, Kenji Komatsu, Takahiro Sugiura, Shoujiro Ogawa, M. Satoh, F. Nomura","doi":"10.5702/massspectrometry.S0051","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0051","url":null,"abstract":"A method for the simultaneous determination of 25-hydroxyvitamin D3 [25(OH)D3] and its 3-sulfate [25(OH)D3S] in newborn plasma, which is expected to be helpful in the assessment of the vitamin D status, using stable isotope-dilution liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) has been developed and validated. The plasma was pretreated based on the deproteinization and solid-phase extraction, then subjected to derivatization with 4-(4-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD). The derivatization enabled the accurate quantification of 25(OH)D3 without interference from 3-epi-25(OH)D3 and also facilitated the simultaneous determination of the two metabolites by LC/positive ESI-MS/MS. Quantification was based on the selected reaction monitoring with the characteristic fragmentation of the DAPTAD-derivatives during MS/MS. This method was reproducible (intra- and inter-assay relative standard deviations of 7.8% or lower for both metabolites) and accurate (analytical recovery, 95.4-105.6%). The limits of quantification were 1.0 ng/mL and 2.5 ng/mL for 25(OH)D3 and 25(OH)D3S, respectively, when using a 20-μL sample. The developed method was applied to the simultaneous determination of plasma 25(OH)D3 and 25(OH)D3S in newborns; it was recognized that the plasma concentration of 25(OH)D3S is significantly higher than that of 25(OH)D3, and preterm newborns have lower plasma 25(OH)D3S concentrations than full-term newborns.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"2016 1","pages":"S0051"},"PeriodicalIF":0.0,"publicationDate":"2016-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88450531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-15DOI: 10.5702/massspectrometry.A0042
K. Sumitomo, Hiroaki Akutsu, Syusei Fukuyama, A. Minoshima, Shin Kukita, Yuji Yamamura, Yoshiaki Sato, Taiki Hayasaka, Shinobu Osanai, H. Funakoshi, N. Hasebe, Masao Nakamura
Conifer and broadleaf trees emit volatile organic compounds in the summer. The major components of these emissions are volatile monoterpenes. Using solid phase microextraction fiber as the adsorbant, monoterpenes were successfully detected and identified in forest air samples. Gas chromatography/mass chromatogram of monoterpenes in the atmosphere of a conifer forest and that of serum from subjects who were walking in a forest were found to be similar each other. The amounts of α-pinene in the subjects became several folds higher after forest walking. The results indicate that monoterpenes in the atmosphere of conifer forests are transferred to and accumulate in subjects by inhalation while they are exposed to this type of environment.
{"title":"Conifer-Derived Monoterpenes and Forest Walking.","authors":"K. Sumitomo, Hiroaki Akutsu, Syusei Fukuyama, A. Minoshima, Shin Kukita, Yuji Yamamura, Yoshiaki Sato, Taiki Hayasaka, Shinobu Osanai, H. Funakoshi, N. Hasebe, Masao Nakamura","doi":"10.5702/massspectrometry.A0042","DOIUrl":"https://doi.org/10.5702/massspectrometry.A0042","url":null,"abstract":"Conifer and broadleaf trees emit volatile organic compounds in the summer. The major components of these emissions are volatile monoterpenes. Using solid phase microextraction fiber as the adsorbant, monoterpenes were successfully detected and identified in forest air samples. Gas chromatography/mass chromatogram of monoterpenes in the atmosphere of a conifer forest and that of serum from subjects who were walking in a forest were found to be similar each other. The amounts of α-pinene in the subjects became several folds higher after forest walking. The results indicate that monoterpenes in the atmosphere of conifer forests are transferred to and accumulate in subjects by inhalation while they are exposed to this type of environment.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"334 1","pages":"A0042"},"PeriodicalIF":0.0,"publicationDate":"2015-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75715546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-07-21DOI: 10.5702/massspectrometry.A0040
Y. Sugiura, Kurara Honda, M. Suematsu
In vivo concentrations of cellular signaling mediators such as inflammatory mediators are normally maintained at very low levels due to their strong ability to induce a biological response. The production, diffusion, and decomposition of such mediators are spatio-temporally regulated. Therefore, in order to understand biochemical basis of disease progression and develop new therapeutic strategies, it is important to understand the spatiotemporal dynamics of the signaling mediators in vivo, during the progression of disorders, e.g., chronic inflammatory diseases; however, the lack of effective imaging technology has made it difficult to determine their localizations in vivo. Such characterization requires technical breakthroughs, including molecular imaging methods that are sensitive enough to detect low levels of metabolites in the heterogeneous tissue regions in diseased organs. We and other groups have attempted to fill this technical gap by developing highly sensitive imaging mass spectrometry (IMS) technologies. To date, we have established two key techniques toward this goal, including (i) a sample preparation procedure that has eliminated the problem of the postmortem degradation of labile metabolites, and (ii) on-tissue derivatization of metabolites, which can enhance analyte ionization efficiency. Here, we review recent progress in the development of these technologies as well as how the highly sensitive IMS technique has contributed to increasing understanding of the biochemical basis of disease mechanisms, discovery of new diagnostic markers, and development of new therapies.
{"title":"Development of an Imaging Mass Spectrometry Technique for Visualizing Localized Cellular Signaling Mediators in Tissues.","authors":"Y. Sugiura, Kurara Honda, M. Suematsu","doi":"10.5702/massspectrometry.A0040","DOIUrl":"https://doi.org/10.5702/massspectrometry.A0040","url":null,"abstract":"In vivo concentrations of cellular signaling mediators such as inflammatory mediators are normally maintained at very low levels due to their strong ability to induce a biological response. The production, diffusion, and decomposition of such mediators are spatio-temporally regulated. Therefore, in order to understand biochemical basis of disease progression and develop new therapeutic strategies, it is important to understand the spatiotemporal dynamics of the signaling mediators in vivo, during the progression of disorders, e.g., chronic inflammatory diseases; however, the lack of effective imaging technology has made it difficult to determine their localizations in vivo. Such characterization requires technical breakthroughs, including molecular imaging methods that are sensitive enough to detect low levels of metabolites in the heterogeneous tissue regions in diseased organs. We and other groups have attempted to fill this technical gap by developing highly sensitive imaging mass spectrometry (IMS) technologies. To date, we have established two key techniques toward this goal, including (i) a sample preparation procedure that has eliminated the problem of the postmortem degradation of labile metabolites, and (ii) on-tissue derivatization of metabolites, which can enhance analyte ionization efficiency. Here, we review recent progress in the development of these technologies as well as how the highly sensitive IMS technique has contributed to increasing understanding of the biochemical basis of disease mechanisms, discovery of new diagnostic markers, and development of new therapies.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"16 1","pages":"A0040"},"PeriodicalIF":0.0,"publicationDate":"2015-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81586495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-07-07DOI: 10.5702/massspectrometry.A0041
L. Chen
In a tutorial paper on the application of free-jet technique for API-MS, John Fenn mentioned that "…for a number of years and a number of reasons, it has been found advantageous in many situations to carry out the ionization process in gas at pressures up to 1000 Torr or more" (Int. J. Mass Spectrom. 200: 459-478, 2000). In fact, the first ESI mass spectrometer constructed by Yamashita and Fenn had a counter-flow curtain gas source at 1050 Torr (ca. 1.4 atm) to sweep away the neutral (J. Phys. Chem. 88: 4451-4459, 1984). For gaseous ionization using electrospray plume, theoretical analysis also shows that "super-atmospheric operation would be more preferable in space-charge-limited situations."(Int. J. Mass Spectrom. 300: 182-193, 2011). However, electrospray and the corona-based chemical ion source (APCI) in most commercial instrument are basically operated under an atmospheric pressure ambient, perhaps out of the concern of safety, convenience and simplicity in maintenance. Running the ion source at pressure much higher than 1 atm is not so common, but had been done by a number of groups as well as in our laboratory. A brief review on these ion sources will be given in this paper.
{"title":"When API Mass Spectrometry Meets Super Atmospheric Pressure Ion Sources.","authors":"L. Chen","doi":"10.5702/massspectrometry.A0041","DOIUrl":"https://doi.org/10.5702/massspectrometry.A0041","url":null,"abstract":"In a tutorial paper on the application of free-jet technique for API-MS, John Fenn mentioned that \"…for a number of years and a number of reasons, it has been found advantageous in many situations to carry out the ionization process in gas at pressures up to 1000 Torr or more\" (Int. J. Mass Spectrom. 200: 459-478, 2000). In fact, the first ESI mass spectrometer constructed by Yamashita and Fenn had a counter-flow curtain gas source at 1050 Torr (ca. 1.4 atm) to sweep away the neutral (J. Phys. Chem. 88: 4451-4459, 1984). For gaseous ionization using electrospray plume, theoretical analysis also shows that \"super-atmospheric operation would be more preferable in space-charge-limited situations.\"(Int. J. Mass Spectrom. 300: 182-193, 2011). However, electrospray and the corona-based chemical ion source (APCI) in most commercial instrument are basically operated under an atmospheric pressure ambient, perhaps out of the concern of safety, convenience and simplicity in maintenance. Running the ion source at pressure much higher than 1 atm is not so common, but had been done by a number of groups as well as in our laboratory. A brief review on these ion sources will be given in this paper.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"9 1","pages":"A0041"},"PeriodicalIF":0.0,"publicationDate":"2015-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86748617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-07-02DOI: 10.5702/massspectrometry.A0039
Kazuki Yamamoto, Yoko Chikaoka, Gosuke Hayashi, Ryosuke Sakamoto, Ryuji Yamamoto, A. Sugiyama, T. Kodama, A. Okamoto, T. Kawamura
Mass spectrometric proteomics is an effective approach for identifying and quantifying histone post-translational modifications (PTMs) and their binding proteins, especially in the cases of methylation and acetylation. However, another vital PTM, phosphorylation, tends to be poorly quantified because it is easily lost and inefficiently ionized. In addition, PTM binding proteins for phosphorylation are sometimes resistant to identification because of their variable binding affinities. Here, we present our efforts to improve the sensitivity of detection of histone H4 tail peptide phosphorylated at serine 1 (H4S1ph) and our successful identification of an H4S1ph binder candidate by means of a chemical proteomics approach. Our nanoLC-MS/MS system permitted semi-quantitative label-free analysis of histone H4 PTM dynamics of cell cycle-synchronized HeLa S3 cells, including phosphorylation, methylation, and acetylation. We show that H4S1ph abundance on nascent histone H4 unmethylated at lysine 20 (H4K20me0) peaks from late S-phase to M-phase. We also attempted to characterize effects of phosphorylation at H4S1 on protein-protein interactions. Specially synthesized photoaffinity bait peptides specifically captured 14-3-3 proteins as novel H4S1ph binding partners, whose interaction was otherwise undetectable by conventional peptide pull-down experiments. This is the first report that analyzes dynamics of PTM pattern on the whole histone H4 tail during cell cycle and enables the identification of PTM binders with low affinities using high-resolution mass spectrometry and photo-affinity bait peptides.
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