An Extension to the JCAMP-DX Standard File Format, JCAMP-DX V.5.01

1999 ◽  
Vol 71 (8) ◽  
pp. 1549-1556 ◽  
Author(s):  
Peter Lampen ◽  
Jörg Lambert ◽  
R. J. Lancashire ◽  
R. S. McDonald ◽  
P. S. McIntyre ◽  
...  

Version 5.00 of the JCAMP-DX specifications were published for NMR and Mass Spectrometry file formats in Appl. Spectrosc.47, 1093-1099, (1993) and Appl. Spectrosc.48, 1545-1552, (1994). Since publication of these protocols developments in spectroscopy have led to a large number of requests for additions for applications not originally covered. Following careful consideration, it has become apparent that a few minor modifications will significantly increase the range of possible applications.In addition, new data labels have been introduced to ensure that files are year 2000 compliant and allow for conformity with good laboratory practices (GLP). These modifications are detailed in this publication as well as examples of the official NTUPLE JCAMP-DX definition as applied to NMR data.

2019 ◽  
Author(s):  
Niels Hulstaert ◽  
Timo Sachsenberg ◽  
Mathias Walzer ◽  
Harald Barsnes ◽  
Lennart Martens ◽  
...  

AbstractThe field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.


2012 ◽  
Vol 31 (4) ◽  
pp. 46 ◽  
Author(s):  
Eun G Park ◽  
Sam Oh

This study examines the attributes that have been used to assess file formats in literature and compiles the most frequently used attributes of file formats in order to establish open standard file format selection criteria.  A comprehensive review was undertaken to identify the current knowledge regarding file format selection criteria. The findings indicate that the most common criteria can be categorized into five major groups: functionality, metadata, openness, interoperability and independence. These attributes appear to be closely related. Additional attributes include presentation, authenticity, adoption, protection, preservation, reference and others. 


Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 65
Author(s):  
Byeoung-Kyu Choi ◽  
Duk-Yeon Cho ◽  
Dong-Kug Choi ◽  
Phan Thi Hoai Trinh ◽  
Hee Jae Shin

Two new phomaligols, deketo-phomaligol A (1) and phomaligol E (2), together with six known compounds (3–8) were isolated from the culture broth of the marine-derived fungus Aspergillus flocculosus. Compound 1 was first isolated as a phomaligol derivative possessing a five-membered ring. The structures and absolute configurations of the new phomaligols were determined by detailed analyses of mass spectrometry (MS), nuclear magnetic resonance (NMR) data, optical rotation values and electronic circular dichroism (ECD). In addition, the absolute configurations of the known compounds 3 and 4 were confirmed by chemical oxidation and comparison of optical rotation values. Isolated compounds at a concentration of 100 μM were screened for inhibition of nitric oxide (NO) production in lipopolysaccharide (LPS)-induced BV-2 microglial cells. Among the compounds, 4 showed moderate anti-neuroinflammatory effects with an IC50 value of 56.6 μM by suppressing the production of pro-inflammatory mediators in activated microglial cells without cytotoxicity.


2014 ◽  
Vol 940 ◽  
pp. 433-436 ◽  
Author(s):  
Ying Zhang ◽  
Xin Shi

Based on the detailed analysis of the STL file format, VC++ 6.0 programming language was used to extract the STL ASCII and binary file information, at the same time, using the OpenGL triangle drawing technology for graphical representation of the STL file, with rendering functions such as material, coordinate transformation, lighting, et al, finally realizing the loading and three-dimensional display of STL ASCII and binary file formats.


2021 ◽  
Author(s):  
Renee M. Happs ◽  
Bennett Addison ◽  
Crissa Doeppke ◽  
Bryon S. Donohoe ◽  
Mark F. Davis ◽  
...  

Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and nondestructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.


2013 ◽  
Vol 13 (3) ◽  
pp. 216-220 ◽  
Author(s):  
Anggia Murni ◽  
Novriyandi Hanif ◽  
Junichi Tanaka

One new dolabellane (1) and two known diterpenoids stolonidiol (2) and clavinflol B (3) have been isolated from the ethyl acetate extract of the Indonesian soft coral Anthelia sp. A new compound 1 exhibited a moderate cytotoxicity against NBT-T2 cells at 10 µg/mL, while known compounds 2 and 3 showed cytotoxicity at 1 and 0.5 µg/mL, respectively. Structure of the new compound 1 was elucidated by interpretation of NMR spectroscopic data (1D and 2D NMR data) and mass spectrometry (ESIMS data) as well as comparison with those of related ones. This finding should be useful for anti cancer drug development of the promising dolabellane-types compound.


1986 ◽  
Vol 64 (4) ◽  
pp. 831-836 ◽  
Author(s):  
Jean Claude Caille ◽  
Michel Farnier ◽  
Roger Guilard ◽  
André Aubry ◽  
Claude Lecomte
Keyword(s):  
X Ray ◽  
Nmr Data ◽  

Synthesis of two cyclopentenic δ-lactones, 1,3,4,4a,5,6-hexahydrocyclopenta[c]pyran-1-one and its analogue possessing a cyclopentenyl group bonded to the carbon atom 4a is described, starting from the cyclopentanone or cyclopentylidene cyclopentanone. The remarkable reactivity of the tosylhydrazones allows transformation of these compounds into substituted cyclopentenes, which lead to δ-lactones by cyclization. The conditions of cyclization depend on the nature of the cyclopentanone. The structure of the two δ-lactones is established by 1H and 13C nmr data, mass spectrometry, and, in one case, by X-ray analysis.


1976 ◽  
Vol 54 (13) ◽  
pp. 2135-2140 ◽  
Author(s):  
J. Dazord ◽  
H. Mongeot ◽  
H. Atchekzai ◽  
J. P. Tuchagues

The mixed halide–pseudohalides BXn(NCS)3−n (n = 1 or 2) have been obtained except for X = F. Mixtures of these compounds with boron trihalide and boron triisothiocyanate are prepared by the reaction of BX3 either with metal isothiocyanates or with boron triisothiocyanate. Mass spectrometry, infrared, Raman, and 11B nmr data are reported. Rapid redistribution reactions prevent the isolation of the mixed species. Vibration spectrometry shows that boron is bonded to the nitrogen of the NCS group and not to the sulfur.


2018 ◽  
pp. 218-233
Author(s):  
Mayank Yuvaraj

During the course of planning an institutional repository, digital library collections or digital preservation service it is inevitable to draft file format policies in order to ensure long term digital preservation, its accessibility and compatibility. Sincere efforts have been made to encourage the adoption of standard formats yet the digital preservation policies vary from library to library. The present paper is based against this background to present the digital preservation community with a common understanding of the common file formats used in the digital libraries or institutional repositories. The paper discusses both open and proprietary file formats for several media.


2006 ◽  
Vol 78 (3) ◽  
pp. 613-631 ◽  
Author(s):  
Richard Cammack ◽  
Yang Fann ◽  
Robert J. Lancashire ◽  
John P. Maher ◽  
Peter S. McIntyre ◽  
...  

In this document, we define a data exchange format initially formulated from discussions of an International Union of Pure and Applied Chemistry (IUPAC) limited-term task group at the 35th Royal Society of Chemistry-ESR conference in Aberdeen 2002. The definition of this format is based on the IUPAC Joint Committee on Atomic and Molecular Physical Data Exchange (JCAMPDX) protocols, which were developed for the exchange of infrared spectra and extended to chemical structures, nuclear magnetic resonance data, mass spectra, and ion mobility spectra. This standard of the JCAMP-DX was further extended to cover year 2000 compatible date strings and good laboratory practice, and the next release will cover the information needed for storing n-dimensional data sets. The aim of this paper is to adapt JCAMP-DX to the special requirements for electron magnetic resonance (EMR).


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