| 1. |
- Fukuda, Tetsuya, et al.
(författare)
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A selected reaction monitoring mass spectrometric assessment of biomarker candidates diagnosing large-cell neuroendocrine lung carcinoma by the scaling method using endogenous references
- 2017
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:4
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Tidskriftsartikel (refereegranskat)abstract
- Selected reaction monitoring mass spectrometry (SRM-MS) -based semi-quantitation was performed to assess the validity of 46 selected candidate proteins for specifically diagnosing large-cell neuroendocrine lung carcinoma (LCNEC) and differentiating it from other lung cancer subtypes. The scaling method was applied in this study using specific SRM peak areas (AUCs) derived from the endogenous reference protein that normalizes all SRM AUCs obtained for the candidate proteins. In a screening verification study, we found that seven out of the 46 candidate proteins were statistically significant for the LCNEC phenotype, including 4F2hc cell surface antigen heavy chain (4F2hc/CD98) (p-ANOVA ≤ 0.0012), retinal dehydrogenase 1 (p-ANOVA ≤ 0.0029), apolipoprotein A-I (p-ANOVA ≤ 0.0004), β-enolase (p-ANOVA ≤ 0.0043), creatine kinase B-type (p-ANOVA ≤ 0.0070), and galectin- 3-binding protein (p-ANOVA = 0.0080), and phosphatidylethanolamine-binding protein 1 (p-ANOVA ≤ 0.0012). In addition, we also identified candidate proteins specific to the smallcell lung carcinoma (SCLC) subtype. These candidates include brain acid soluble protein 1 (p-ANOVA < 0.0001) and γ-enolase (p-ANOVA ≤ 0.0013). This new relative quantitationbased approach utilizing the scaling method can be applied to assess hundreds of protein candidates obtained from discovery proteomic studies as a first step of the verification phase in biomarker development processes.
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| 2. |
- Fukuda, Tetsuya, et al.
(författare)
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An Improvement on MS-based Epigenetic Analysis of Large Histone-derived Peptides by Using the IVU Interface.
- 2015
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 1096-0309 .- 0003-2697. ; 486:Online 05 June 2015, s. 14-16
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Tidskriftsartikel (refereegranskat)abstract
- Highly protonated histone-derived peptides impede a sufficient mass spectrometry (MS) -based epigenetic analysis since their relatively low m/z due to a high degree of proton addition to peptides would difficult to analyze the resulting complex MS/MS spectra. In order to reduce the degree of protonations, we have developed a new interface, the IVU, in which peptides are ionized under a vaporized organic solvent, and it has demonstrated that the doubly-charged histone-tail H2B peptide, PEPAKSAPAPKKGSKKAVTKAQKK (m/z 1238.243 , +2), has been detected by using the IVU interface and sequenced, which was not detectable before.
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| 3. |
- Nakayama, Noboru, et al.
(författare)
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Developments of mass spectrometry-based technologies for effective drug development linked with clinical proteomes.
- 2016
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Ingår i: Drug Metabolism and Pharmacokinetics. - : Elsevier BV. - 1347-4367. ; 31:1, s. 3-11
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Forskningsöversikt (refereegranskat)abstract
- A strong demand in drug discovery and development today is to overcome "Big Gaps" encountered by differences in species and races, to accelerate effective developments in cost and time, and to meet medical needs. Moreover, drugs of various types have emerged which cover middle-size molecules and polymers rather than conventional small molecules. Upon those challenges, mass spectrometry (MS)-based technologies, which will be described in this paper, will play an increasingly important role, among which the liquid chromatography-tandem mass spectrometry (LC/MS/MS) platform will be powerful as rapid and molecule-based analysis more than ever. nanoPore Optical Interferometry (nPOI) newly introduced can detect even weak interactions in protein-protein and protein-compound, and can be connected directly to LC/MS/MS for identification of binding molecular species, which will be quite useful for affinity ranking and high-throughput interaction screening. Imaging MS provides the molecular information and spatial distribution of targeted molecules within a tissue specimen. MS-based clinical proteomics utilizing clinical specimens and empowered by advanced bioinformatics can attain both key protein-protein interaction (PPI) networks with major protein players responsible for functional mechanisms of a disease subtype. An integration of those MS-based technologies will deliver a seamless platform of drug development from molecules identified in human clinical specimens.
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| 4. |
- Sada, Y., et al.
(författare)
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Structure near the K- + p + p threshold in the in-flight 3He(K-, Λp)n reaction
- 2016
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Ingår i: Progress of Theoretical and Experimental Physics. - : Oxford University Press (OUP). - 2050-3911. ; 2016:5
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Tidskriftsartikel (refereegranskat)abstract
- To search for an S = -1 di-baryonic state which decays toΛp, the 3He(K-,Λp)nmissing reaction was studied at 1.0 GeV/c. Unobserved neutrons were kinematically identified from the missing mass MX of the 3He (K-,Λp) X reaction in order to have a large acceptance for the Λpn final state. The observed Λpn events, distributed widely over the kinematically allowed region of the Dalitz plot, establish that the major component comes from a three-nucleon absorption process. A concentration of events at a specific neutron kinetic energy was observed in a region of low momentum transfer to the Λp. To account for the observed peak structure, the simplest S-wave polewas assumed to exist in the reaction channel, having a Breit-Wigner formin energy and with a Gaussian form factor. A minimum X2 method was applied to deduce its mass, MX = 2355+6 -8 (stat.) ±12 (syst.)MeV/c2, and decay width, γX = 110+19 -17 (stat.) ±27 (syst.)MeV/c2, respectively. The form factor parameter QX ∼ 400MeV/c implies that the range of the interaction is about 0.5 fm.
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| 5. |
- Safari, Cecilia, 1989, et al.
(författare)
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Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase
- 2023
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Ingår i: Science advances. - 2375-2548. ; 9:49
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Tidskriftsartikel (refereegranskat)abstract
- Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.
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