ASTM E2078-2000(2016) Standard Guide for Analytical Data Interchange Protocol for Mass Spectrometric Data《质谱数据用分析数据交换协议的标准指南》.pdf

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1、Designation: E2078 00 (Reapproved 2016)Standard Guide forAnalytical Data Interchange Protocol for MassSpectrometric Data1This standard is issued under the fixed designation E2078; the number immediately following the designation indicates the year oforiginal adoption or, in the case of revision, the

2、 year of last revision. A number in parentheses indicates the year of last reapproval. Asuperscript epsilon () indicates an editorial change since the last revision or reapproval.1. Scope1.1 This guide covers the implementation of the MassSpectrometric Data Protocol in analytical software applica-ti

3、ons. Implementation of this protocol requires:1.1.1 Specification E2077, which contains the full set ofdata definitions. The mass spectrometric data protocol is notbased upon any specific implementation; it is designed to beindependent of any particular implementation so that imple-mentations can ch

4、ange as technology evolves. The protocol isimplemented in categories to speed its acceptance throughactual use.1.1.2 Specification E2077 contains a full description of thecontents of the data communications protocol, including theanalytical information categories with data elements and theirattribut

5、es for most aspects of mass spectrometric tests.1.2 The analytical information categories are a practicalconvenience for breaking down the standardization processinto smaller, more manageable pieces. It is easier for develop-ers to build consensus and produce working systems based onsmaller informat

6、ion sets, without the burden and complexity ofthe hundreds of data elements contained in all the categories.The categories also assist vendors and end users in using theguide in their computing environments.1.3 The network common data format (NetCDF) data inter-change system is the container used to

7、 communicate databetween applications in a way that is independent of bothcomputer architectures and end-user applications. In essence, itis a special type of application designed for data interchange.1.4 The common data language (CDL) template for massspectrometry is a language specification of the

8、 mass spectrom-etry dataset being interchanged. With the use of the NetCDFutilities, this human-readable template can be used to generatean equivalent binary file and the software subroutine callsneeded for input and output of data in analytical applications.2. Referenced Documents2.1 ASTM Standards

9、:2E2077 Specification for Analytical Data Interchange Proto-col for Mass Spectrometric Data2.2 Other Standard:NetCDF Users Guide32.3 ISO Standards:48601:1988 Data elements and interchange formats, (Firstedition published 1988-06-15; with Technical Corrigen-dum 1 published 1991-05-01)3. List of Conte

10、nts and Use3.1 NetCDF ToolkitThe protocol is an application pro-gramming interface (API) layered on top of the public domainNetCDF toolkit. NetCDF is a set of tools that facilitate readingor writing platform-independent, self-describing data files. Alldata in a NetCDF file is written using the exter

11、nal datarepresentation (XDR). XDR was developed by Sun Microsys-tems and is used for platform-independent file systems for allworkstations and personal computers. Each NetCDF dataelement is self-describing - it has a name, type, and dimen-sionality. A NetCDF file contains three parts: a dimensionsse

12、ction, which defines the names and size of all dimensionsused to describe variables; a variables section, which definesthe names, data types, dimensionality, and attributes for allvariables used in the file; and finally, a data section, whichcontains the actual values assigned to the variables. Attr

13、ibutesare numbers or strings which augment the description ofvariables or the file as a whole.3.1.1 For example, a variable “x_axis_ values” might con-tain an array of numbers representing the abscissa of atwo-dimensional data set. It would have a dimension, possiblynamed “x_axis_size,” which would

14、specify the number of1This guide is under the jurisdiction of ASTM Committee E13 on MolecularSpectroscopy and Separation Science and is the direct responsibility of Subcom-mittee E13.15 on Analytical Data.Current edition approved April 1, 2016. Published June 2016. Originallyapproved in 2000. Last p

15、revious edition approved in 2010 as E2078 00 (2010).DOI: 10.1520/E2078-00R16.2For referenced ASTM standards, visit the ASTM website, www.astm.org, orcontact ASTM Customer Service at serviceastm.org. For Annual Book of ASTMStandards volume information, refer to the standards Document Summary page ont

16、he ASTM website.3Available from Russell K. Rew, Unidata Program Center, University Corpora-tion for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307-3000, http:/www.unidata.ucar.edu/.4Available from International Organization for Standardization (ISO), ISOCentral Secretariat, BIBC II, Chemin d

17、e Blandonnet 8, CP 401, 1214 Vernier,Geneva, Switzerland, http:/www.iso.org.Copyright ASTM International, 100 Barr Harbor Drive, PO Box C700, West Conshohocken, PA 19428-2959. United States1abscissa points. The variable might have some descriptiveattributes, such as “units” (with a value of“ Seconds

18、,” perhaps),“scale_factor” (with a value of 1000.0, specifying that allstored abscissa values should be multiplied by 1000.0 to get theactual value), or “long_name” (with value“ Time”, whichmight be used to label the abscissa when drawing a plot).3.1.2 The NetCDF toolkit has been placed in the publi

19、cdomain by the Unidata Program Center, a non-profit softwaresupport organization for the University Corporation for Atmo-spheric Research. The Unidata Program Center is funded bythe National Science Foundation, National Center for Atmo-spheric Research, and other organizations and provides ongo-ing

20、development and support of NetCDF and related tools.3.1.3 The NetCDF version currently supported in thisimplementation is 2.3.2.3.2 Data StructuresEach of the analytical informationclass tables in the specification document has a correspondingdata structure; however, not every field in each table ha

21、s acorresponding data element in a structure, and the data struc-tures may have elements that do not appear in any class table.Most of these differences are due to details of the implemen-tation which could not be hidden.3.2.1 The data structures provide the mapping between theattribute name and dat

22、a type described in the specification andthe field and actual data type in the file. The actual NetCDFdimension, variable, and attribute names are hidden from theAPI level. These names in fact are irrelevant for applicationprograms; it is the data structure which provides the informa-tion interchang

23、e between the application and the file.3.2.2 Each data structure and its mapping to an analyticalinformation class are described in detail later in this guide.3.2.3 Application Programming Interface Functions:3.2.3.1 The application programming interface providesprogrammatic access to the contents o

24、f the files. Mass spectraldata occurs in three forms: global information, which relates tothe contents of the entire file, information which describes eachpart of a multi-component instrument, and information whichchanges on a scan-by-scan basis for spectra and library entries.API functions are prov

25、ided for opening a file for reading orwriting; closing a file; reading and writing global, per-component instrument, and per-scan spectral and library infor-mation; initializing and clearing data structure contents; and afew miscellaneous utility functions. Each of these functions isdescribed in det

26、ail in a later section of this guide.3.2.4 Enumerated SetsMany of the attributes listed in theAnalytical Data Interchange Protocol for Mass SpectrometricData specification have an enumerated set of associated values.The attribute may take only one value from that restricted set.In the implementation

27、, each such attribute is defined as aformal C type, and the allowed values are defined as anenumerated set of that formal type. Each enumerated value isassociated with a unique string literal, and it is these stringliterals, not the enumeration values, which are written to orread from the file. This

28、 practice both enforces the use of theproper enumeration values and follows the NetCDF dictumthat files be self-describing. If the enumeration values werewritten instead of the strings, then some lookup mechanismwould be required external to the NetCDF file to translate thenumber into something mean

29、ingful.4. Conventions4.1 The format convention adopted in this guide is asfollows:(1) Normal text is presented in this font (Times NewRoman).(2) API symbols (functions, formal types, etc.) are pre-sented in boldface Helvetica font.(3) Parameters to API functions are presented in italicHelvetica font

30、.(4) Example code is presented in normal Helvetica font.4.2 Other ConventionsAll indices begin at zero (C con-vention). In several data structures, a scan_no or inst_noelement must be loaded before reading or writing. Thisidentifies the scan or instrument component number for whichdata will be read

31、or written. In all cases, scan or instrumentcomponent numbers begin at zero.4.2.1 All date/time stamps are formatted using the ISOstandard 8601 format referenced in the specification. An APIutility function is provided for conversion between date/timeinformation in numeric form and ISO-8601 string f

32、ormat (seems_convert_date(), below).5. Mass Spectrometric Data Protocol Distribution Kit5.1 It is intended that potential users of this implementationcan obtain a complete NetCDF and API distribution kit fromvarious instrument vendors websites. Information on how toobtain the kit will be posted on t

33、he ASTM website(www.astm.org) under Committee E01.25.5.2 The Analytical Data Interchange Protocol for MassSpectrometric Data distribution kit contains:5.2.1 SoftwareNetCDF distribution kit from Unidata(with the modified makefile needed to make the kit compile outof the box).5.2.2 NetCDF Users Guides

34、upplied by Unidata ProgramCenter.5.2.3 Specification E2077.5.2.4 Guide E2078.6. Hardware and Software6.1 This section describes the hardware and software con-figurations used for testing. In general, the NetCDF systemputs very few requirements on the hardware because mostroutines are left on disk. O

35、nly routines being used at anyparticular time are kept in memory.Any limitations found weretypically those not imposed by NetCDF but ones imposed bythe operating system or environment.6.1.1 Hardware (Personal Computers)The personal com-puter system hardware originally used for testing was:6.1.1.1 In

36、tel 80286 processor,6.1.1.2 640K minimum,6.1.1.3 Monochrome, EGA, VGA graphics,6.1.1.4 20 megabyte minimum, 80 megabyte hard-disk istypical, and6.1.1.5 A mouse (optional).E2078 00 (2016)26.1.1.6 NetCDF works well on AT-class machines andhigher. NetCDF does not have the items in 6.1.1.1 6.1.1.5 asreq

37、uirements. These are just the minimum, base-level systemsthat were used.6.1.2 SoftwareNetCDF runs on MS-DOS, OS/2,Macintosh, Windows 95, and Windows NT operating systemsfor personal computers. NetCDF was originally ported fromUNIX to DOS running on an IBM-PS/2 Model 80. It wasrecently ported to the

38、Macintosh OS. NetCDF is written in theC programming language, and there are FORTRAN jacketsavailable for applications that want to use FORTRAN calls.The personal computer software originally employed for test-ing and developing NetCDF applications was:6.1.2.1 Microsoft DOS V3.3 or above,6.1.2.2 Micr

39、osoft C Compiler V6.0,6.1.2.3 Microsoft Windows V3.0,6.1.2.4 Microsoft Windows SDK, and6.1.2.5 NetCDF Version 2.0.1.6.1.3 Workstations and ServersNetCDF runs easily onUNIX workstations such as Sun 3, Sun 4, VAXstations,DECstation 3100, VAXstation II running ULTRIX or VMS,and IBM RS/6000. There are n

40、o particular hardware require-ments for workstation class machines, since all workstationshave the minimum hardware outlined for personal computersin 6.1.1.7. Significance and Use7.1 General Coding GuidelinesThe NetCDF libraries aresupplied to developers as source code. End users receive thelibrarie

41、s in compiled binary form as part of a vendorsapplication.7.1.1 Developers setting out to write a program to converttheir data files to the Mass Spectrometric Data Protocol shouldconsider using the NetCDF utilities ncgen and ncdump. Afterdevelopers create the NetCDF file they should use the ncdumppr

42、ogram to generate the ASCII representation of the data file,and examine it to ensure the data are being correctly put intothe file.7.2 Make Files for NetCDF Libraries and UtilitiesIngeneral the compilation is straightforward. The make files weremodified after they were received from the UnidataCorpo

43、ration, because they did not compile the first time onPCs. The changes needed to get the Unidata distribution to runon DOS are (1) rename the file MAKEFILE to UNIX.MK, and(2) rename MSOFT.MK to MAKEFILE, and then runNMAKE. The default switches in the Unidata distribution usethe switches for the floa

44、ting point coprocessor and MicrosoftWindows options.7.2.1 The protocol kit contains some complete makefileexamples for Microsoft C V6.0 running on DOS. The Micro-soft C V6.0 compiler manual should be consulted for the exactmeaning of the compiler and linker options.7.2.2 The VMS and SunOS compilatio

45、n instructions are indirectories for those operating systems.7.3 NetCDF Library Build OrderThe NetCDF librariesmust be built in a specific order. The correct order to build theNetCDF directories is:UTILXDRSRCNCDUMPNCGENNCTEST7.3.1 The UTIL and XDR makefiles work as distributedusing NMAKE with Micros

46、oft C V6.0.8. CDL Template Structure8.1 A NetCDF template is built from CDL statements and isstructured into three sections: (1) dimension declarations, (2)variable declarations, and (3) the data section.8.2 Afew points of clarification about the CDLlanguage aregiven here to facilitate its understan

47、ding. For more in-depthinformation on CDL, please consult the NetCDF Users Guide.8.2.1 A NetCDF template starts with the word “NetCDF”followed by the dataset name.8.2.2 CDL comments are indicated by two forward slashcharacters (/).8.2.3 Section indicators (dimensions:, variables:, and data:)end with

48、 a colon character (:). These are the only tokens thatend with a colon character.8.2.4 Statements within sections end with the semicoloncharacter (;).8.2.5 Variable names beginning with numbers must bepreceded by an underline character (_). Otherwise the ncgenparser will flag an error.8.2.5.1 Underl

49、ine characters were chosen for this protocolover hyphen characters, because some compilers may interprethyphens as subtraction operators. The feature of CDL thatallows implicit numerical datatyping of attributes in not beingused in the first version of the template. Instead, all floatingpoint attributes are being handled as strings. This forcesprogrammers to explicitly type variables, thereby encouragingmore deliberate programming styles. For example:aia_template_revision = “0.8”; /M12345:netcdf_revision = “2.0.1”; /M12345Consult the NetCDF Users Guide for