Construction of a Mass Spectrum Library Containing Predicted Electron Ionization Mass Spectra Prepared Using a Machine Learning Model and the Development of an Efficient Search Method.

Electron ionization (EI) mass spectrum library searching is usually performed to identify a compound in gas chromatography/mass spectrometry. However, compounds whose EI mass spectra are registered in the library are still limited compared to the popular compound databases. This means that there are compounds that cannot be identified by conventional library searching but also may result in false positives. In this report, we report on the development of a machine learning model, which was trained using chemical formulae and EI mass spectra, that can predict the EI mass spectrum from the chemical structure. It allowed us to create a predicted EI mass spectrum database with predicted EI mass spectra for 100 million compounds in PubChem. We also propose a method for improving library searching time and accuracy that includes an extensive mass spectrum library.

Integrated qualitative analysis of polymer sample by pyrolysis-gas chromatography combined with high-resolution mass spectrometry: Using accurate mass measurement results from both electron ionization and soft ionization.

RATIONALE: Gas chromatography/mass spectrometry (GC/MS) is a powerful analytical tool used to separate and then identify volatile compounds through library database searches. However, as not all compounds are registered in these databases, it is not uncommon to detect unregistered components. Therefore, new analytical techniques were developed that utilize methods of identification beyond database searches alone. METHODS: Acquire data by using electron ionization (EI) and soft ionization (SI) with high-resolution mass spectrometry (HRMS). Use the EI mass spectra to library search for matches. Use the SI mass spectra for accurate mass analysis of the EI molecular ions. Conduct an isotope pattern analysis of the molecular ion to refine the possible candidate compositions. Use these compositions as a constraint for the accurate mass analysis of the EI fragment ions. If a given molecular ion formula is not correct, the EI fragment ions will not show good matches. Finally, all analytical results are integrated into a color-coded qualitative analysis report. RESULTS: The capabilities of this new integrated analytical method were assessed for a polymer resin sample that was measured by using pyrolysis-gas chromatography/high resolution time-of-flight mass spectrometry. A total of 161 compounds were detected in the total ion current chromatogram, and 154 of these compounds were identified as having only one chemical formula candidate with this new integrated qualitative analysis method. CONCLUSIONS: This new integrated qualitative analysis method gives analytical results independent of library search results. It can be applied to a variety of SI methods including chemical ionization, photoionization, field ionization, and low-energy EI.

Matrix-Assisted Laser Desorption Ionization Imaging Mass Spectrometry of Drug Distribution in Mouse Brain Tissue by High-Resolution Time-of-Flight Mass Spectrometry.

Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the opportunity to visualize the distributions of drugs and metabolites in tissue specimens without requiring radioisotopes, as are used for whole-body autoradiography. However, the analysis of low-molecular-weight compounds is often difficult using the common reflectron-type MALDI time-of-flight mass spectrometers. Insufficient mass resolving power causes overlapping of the target drug peak with matrix compound or surface contaminant peaks. To solve this issue, we describe the procedure for imaging mass spectrometry using a high-mass-resolution mass spectrometer that can separate isobaric peaks.

Upper-limb motor and sensory function in patients with hip fracture: Comparison with community-dwelling older adults.

BACKGROUND: Upper-limb function is important in patients with hip fracture so they can perform activities of daily living and participate in leisure activities. Upper-limb function of these patients, however, has not been thoroughly investigated. OBJECTIVE: The aim of this study was to evaluate the upper-limb motor and sensory functions in patients with hip fracture by comparing these functions with those of community-dwelling older adults (control group). METHODS: We compared the results of motor and sensory function tests of upper-limb function - range of motion, strength, sensibility, finger dexterity, comprehensive hand function - between patients with hip fracture (n= 32) and the control group (n= 32). RESULTS: Patients with hip fracture had significantly reduced grip strength, pinch strength, finger dexterity, and comprehensive hand function compared with the control group. CONCLUSIONS: Most upper-limb functions are impaired in the patients with hip fracture. Thus, upper-limb function of patients with hip fracture should be considered during treatment.

N-Terminal Derivatization with Structures Having High Proton Affinity for Discrimination between Leu and Ile Residues in Peptides by High-Energy Collision-Induced Dissociation.

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.

Exploring the factor on sensory motor function of upper limb associated with executive function in communitydwelling older adults.

Exercise, such as cardiovascular fitness training, has been shown to have utility in improving executive function but is difficult for older adults with low mobility to perform. Accordingly, there is interest in the development of regimens other than high mobility exercises for older adults with low mobility. The aim of the present study was to evaluate the association between sensory motor function of the upper limb and executive function in community-dwelling older adults. A cross-sectional study was conducted in 57 right-handed, independent, community-dwelling older adults. Sensory motor function of upper limb, including range of motion, strength, sensation, finger dexterity, and comprehensive hand function was measured in both hands. Executive function was assessed using the Delta Trail Making Test. Multiple regression analysis indicated the finger dexterity of the non-dominant hand as independently associated with executive function (ß = -0.414, P < 0.001). The findings of the present study may facilitate the development of exercise regimens for improving executive function that are more suitable for older adults with limited physical fitness levels. As this was a cross-sectional study, further studies are required to validate the efficacy of non-dominant finger dexterity training for improving executive function in older adults.

Factors affecting the discharge destination of hip fracture patients who live alone and have been admitted to an inpatient rehabilitation unit.

[Purpose] (1) The aim of this study was to examine relations between clinical and functional assessment and discharge destination and (2) to identify the optimal cutoff point for estimating discharge to home after inpatient rehabilitation. [Subjects] The subjects were 54 hip fracture patients (15 males, 39 females; mean age 81.3 ± 7.4 years) living alone. [Methods] The patients were classified into two groups: those discharged to home and those admitted to an institution. Age, gender, side of fracture, fracture type, number of comorbidities, Functional Independence Measure motor score, and Functional Independence Measure cognitive score were compared between groups. Multiple logistic regression analysis was conducted with discharge to home as the dependent variable and age, gender, side of fracture, fracture type, number of comorbidities, Functional Independence Measure motor score, and Functional Independence Measure cognitive score as independent variables. A receiver operating characteristic curve analysis was used to identify a cutoff point for classification of the patients into the two groups. [Results] Multiple logistic regression analysis showed that the Functional Independence Measure cognitive score was a significant variable affecting the discharge destination. The receiver operating characteristic curve analysis revealed that discharge to home was predicted accurately by a Functional Independence Measure cognitive score of 23.5. [Conclusion] Information from this study is expected to be useful for determining discharge plans and for the setting of treatment goals.

Separation of Isobaric Compounds Using a Spiral Orbit Type Time-of-Flight Mass Spectrometer, MALDI-SpiralTOF.

The development of a MALDI-TOF mass spectrometer that utilizes spiral ion trajectory, SpiralTOF, is reported. The total flight path length was 17 m, which is five times longer than that in commonly used reflectron ion optical system. The SpiralTOF reduced the dependence of the mass resolving power on the mass of the analyte, while improving the accuracy of the mass measurements. Furthermore, SpiralTOF has two advantages that can be exploited for the separation of minor abundant isobaric components in mass spectra. One is the reduction in chemical background due to the post source decay (PSD), which is achieved through PSD ion elimination by electrostatic sectors contained within the SpiralTOF. The other is that the stabilities of peak positions are improved during mass spectrum accumulation. The peak drift caused by the fine structure of matrix crystals and the small irregularities on the sample surface can be reduced by extending the flight path. In this study, these advantages are demonstrated via the analysis of a block copolymer and mass spectrometry imaging (MSI) of lipids.

Structural analysis of triacylglycerols by using a MALDI-TOF/TOF system with monoisotopic precursor selection.

A new MALDI-TOF/TOF system with monoisotopic precursor selection was applied to the analysis of triacylglycerols in an olive oil sample. Monoisotopic precursor selection made it possible to obtain product-ion mass spectra without interference from species that differed by a single double bond. Complete structure determination of all triacylglycerols, including structural isomers, was made possible by interpreting the charge-remote fragmentation resulting from high-energy collision-induced dissociation (CID) of the sodiated triacylglycerols.

Detailed structural analysis of lipids directly on tissue specimens using a MALDI-SpiralTOF-Reflectron TOF mass spectrometer.

Direct tissue analysis using a novel tandem time-of-flight (TOF-TOF) mass spectrometer is described. This system consists of a matrix-assisted laser desorption/ionization ion source, a spiral ion trajectory TOF mass spectrometer "SpiralTOF (STOF)", a collision cell, and an offset parabolic reflectron (RTOF). The features of this system are high precursor ion selectivity due to a 17-m flight path length in STOF and elimination of post-source decay (PSD) ions. The acceleration energy is 20 keV, so that high-energy collision-induced dissociation (HE-CID) is possible. Elimination of PSD ions allows observation of the product ions inherent to the HE-CID process. By using this tandem TOF instrument, the product ion spectrum of lipids provided detailed structural information of fatty acid residues.

Mass Spectrometry Imaging and Structural Analysis of Lipids Directly on Tissue Specimens by Using a Spiral Orbit Type Tandem Time-of-Flight Mass Spectrometer, SpiralTOF-TOF.

In this paper, we report the use of mass spectrometry imaging and structural analysis of lipids directly on a tissue specimen, carried out by means of matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry, using a combination of spiral orbit-type and reflectron-type time-of-flight mass spectrometers. The most intense peak observed in the mass spectrum from a brain tissue specimen was confirmed as phosphatidylcholine (34 : 1) [M+K](+), using tandem mass spectrometry. The charge remote fragmentation channels, which are characteristically observed using high-energy collision-induced dissociation, contributed significantly to this confirmation. Accurate mass analysis was further facilitated by mass correction using the confirmed peak. In mass spectrometry imaging, the high resolving power of our system could separate doublet peak of less than 0.1 u difference, which would otherwise be problematic when using a low-resolution reflectron type time-of-flight mass spectrometer. Two compounds, observed at m/z 848.56 and 848.65, were found to be located in complementary positions on a brain tissue specimen. These results demonstrate the importance of a high-performance tandem time-of-flight mass spectrometer for mass spectrometry imaging and analysis of observed compounds, to allow distinction between biological molecules.

Tandem time-of-flight mass spectrometer with high precursor ion selectivity employing spiral ion trajectory and improved offset parabolic reflectron.

In this study, we have developed a tandem time-of-flight mass spectrometry (TOF/TOF) technique involving the use of a matrix-assisted laser desorption/ionization ion source that exhibits high precursor ion selectivity. An ion optical system with a 17 m spiral ion trajectory was used in the first time-of-flight mass spectrometer. High precursor ion selectivity was achieved by realizing a 15 m flight path, which is considerably longer than that of the conventional MALDI-TOF/TOF before the precursor ion selection by an ion gate; monoisotopic ions could be selected properly up to m/z 2500. Furthermore, the first time-of-flight mass spectrometer was composed of electrostatic sectors and could eliminate post-source decay (PSD) ions. Precursor ions with 20 keV kinetic energy were selected and injected into a collision cell, leading to the generation of fragment ions by high-energy collision-induced dissociation (HE-CID). The optimized second time-of-flight mass spectrometer included a post-acceleration region and an offset parabolic reflectron to record product ion spectra in the entire mass range. Our system could generate a simple HE-CID product ion spectrum because each fragment pathway could be observed as a single peak by the selection of monoisotopic ions of all precursor ions and HE-CID fragment pathways could be predominantly observed by the PSD ion elimination.

Adenoid basal carcinoma arising in the cervical polyp: an immunohistochemical study of stromal cells.

Adenoid basal carcinomas of the uterine cervix are uncommon neoplasms and generally run a favorable clinical course. Although it is well known that these tumors do not evoke the stromal reaction, we immunohistochemically examined a stromal reaction in a case of adenoid basal carcinoma. A 40-year-old woman was found to have a cervical polyp during a medical checkup and underwent polypectomy. Histological examination revealed the finding of adenoid basal carcinoma. Immunohistochemically, a smaller number of CD34-positive and CD31-negative stromal cells, namely fibroblasts, in the stroma of tumor center than in normal cervical stroma were observed. On the other hand, alpha-smooth muscle actin-positive and h-caldesmon-negative stromal cells, namely myofibroblasts, were completely absent in the stroma of tumor center. Finally, our preliminary report suggests that the decrease of CD34-positive fibroblasts in adenoid basal carcinoma may show an early stromal reaction to tumor invasion. Gynecologists and pathologists should bear in mind that adenoid basal carcinoma may arise in a cervical polyp.

Hyaline globule-like structures in undifferentiated sarcoma cells of malignant müllerian mixed tumor of the fallopian tube.

Malignant müllerian mixed tumors (MMMTs) of the fallopian tube are very rare neoplasms, and we present such a case with unusual findings here. A 57-year-old Japanese woman, after she received a medical checkup, underwent salpingo-oophorectomy on the suspicion of ovarian cancer. At the time of operation, the main tumor was present predominantly in the fallopian tube. Microscopically, the tumor consisted of carcinoma and sarcoma components. The carcinoma showed moderately to poorly differentiated adenocarcinoma. The sarcoma consisted of predominantly undifferentiated sarcoma and focally rhabdomyosarcomatous cells with abundant eosinophilic cytoplasm. Immunohistochemically, the differentiation toward rhabdomyosarcoma was confirmed. Interestingly, the cytoplasm of undifferentiated sarcoma cells contained hyaline globule-like structures. These structures showed a positive reaction for PAS, and these structures were not digested by the diastase pretreatment. Ultrastructurally, hyaline globule-like structures corresponded to lysosomes. Finally, pathologists should keep in mind that undifferentiated sarcoma cells in MMMT of the fallopian tube may contain hyaline globule-like structures in the cytoplasm.

Anal canal adenocarcinoma with MUC5AC expression suggestive of anal gland origin.

Anal canal adenocarcinomas arising in the anal ducts or glands are very rare neoplasms, and few useful immunohistochemical markers of these carcinomas are known to date. A 57-year-old man presented with anal bleeding, difficulty of defecation, and anal pain. Macroscopic findings of the surgically resected material showed circular stenosis of the anal canal. The mucosal surface was generally intact, but focal ulceration was seen. Microscopically, the proliferation of adenocarcinoma cells with mucin production was observed in the submucosal and muscular layers. The special stains of periodic acid-Schiff (PAS) and Alcian blue confirmed the presence of neutral and acid mucin. Immunohistochemically, normal rectal-type mucosa and normal anal ducts/glands showed the patterns of cytokeratin 7 (CK7)(-)/CK19(+, focal)/MUC5AC(-) and CK7(+, diffuse)/CK19(+, diffuse)/MUC5AC(+, focal), respectively, and neoplastic cells showed the pattern of CK7(+, diffuse)/CK19(+, diffuse)/MUC5AC(+, focal). Finally, our preliminary report suggests that the immunohistochemical combination of CK7, CK19, and MUC5AC may be an available marker for adenocarcinoma of anal ducts/glands origin.

Frequent retention of heterozygosity for point mutations in p53 and Ikaros in N-ethyl-N-nitrosourea-induced mouse thymic lymphomas.

In agreement with Knudson's two-hit theory, recent findings indicate that the inactivation of tumor suppressor genes is not only mediated by the loss of function but also by the dominant-negative or gain-of-function activity. The former generally accompanies loss of a wild-type allele whereas in the latter a wild-type allele is retained. N-Ethyl-N-nitrosourea (ENU), which efficiently induces point mutations, reportedly leads to the development of tumors by activating ras oncogenes. Little is known about how ENU affects tumor suppressor genes and, therefore, we examined ENU-induced mutations of p53 and Ikaros in thymic lymphomas and compared these with mutations of Kras. In addition, loss of heterozygosity was examined for chromosome 11 to which both p53 and Ikaros were mapped. The frequency of point mutations in p53 and Ikaros was 30% (8/27) and 19% (5/27), respectively, comparable to that observed in Kras (33%: 9/27). In total, 14 of the 27 thymic lymphomas examined (52%) harbored mutations in at least one of these genes. One Ikaros mutation was located at the splice donor site, generating a novel splice isoform lacking zinc finger 3, Ik (F3del). Interestingly, 90% (10/11) of the tumors with point mutations retained wild-type alleles of p53 and Ikaros. Sequence analysis revealed that the most common nucleic acid substitutions were T>A (4/8) in p53, T>C (4/5) in Ikaros and G>A/T (8/9) in Kras, suggesting that the spectrum of mutations was gene dependent. These results suggest that point mutations in tumor suppressor genes without loss of the wild-type allele play an important role in ENU-induced lymphomagenesis.

Effect of carbon ions on life span shortening and tumorigenesis in mice.

One of the important concerns for astronauts in space is cancer risk associated with cosmic radiation, including heavy particle ions. But little information on cancer risk is available. We investigated the effect of carbon ions on life span shortening and tumor induction in B6C3F1 mice. The mice were exposed weekly to 0.4 and 2.0 Gy whole-body carbon-ion- or X-ray-irradiation for 4 consecutive weeks. The spectrum of induced tumors varied depending on the dose. The cause of death was thymic lymphomas and liver tumors at high and low dose, respectively. The life span shortening by X-rays was proportional to dose, while carbon ions produced a convex upward relationship. The relative biological effectiveness for the 50% life span shortening was about 1.4. The large effect of carbon ions encourages the study on tumor induction at low doses in the space.

Loss of heterozygosity in heavy-ion-induced murine T-cell lymphomas.

One of the important concerns for astronauts in space environment is cancer risk associated with cosmic radiation, including heavy particle carbon-ions. But little information on cancer risk is available. In the present study, we investigated the induction of and cellular and molecular characteristics of T-cell lymphomas of B6C3F1 mice induced by carbon-ions and X-rays. The incidence, the latent period and the surface expression of T-cell differentiation antigens were similar between carbon-ion- and X-ray-induced lymphomas. The size of T-cell lymphomas induced by carbon-ions was significantly smaller than that by X-rays. Molecular analysis indicated that high frequency of loss of heterozygosity (LOH) was found on chromosomes 4, 11, 12 and 19 in both lymphomas. Interestingly, the frequency of LOH on chromosome 11 was much higher, but that on chromosome 12 was lower in carbon-ion-induced T-cell lymphomas than in X-ray-induced ones. These results indicate that mechanistic differences may exist between carbon-ion- and X-ray-induced lymphomagenesis.