1、Designation: E2077 00 (Reapproved 2010)Standard Specification forAnalytical Data Interchange Protocol for MassSpectrometric Data1This standard is issued under the fixed designation E2077; the number immediately following the designation indicates the year oforiginal adoption or, in the case of revis
2、ion, the 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 specification covers a standardized format for massspectrometric data representation and a softw
3、are vehicle toeffect the transfer of mass spectrometric data between instru-ment data systems. This specification provides a protocoldesigned to benefit users of analytical instruments and increaselaboratory productivity and efficiency.1.2 The protocol in this specification provides a standard-ized
4、format for the creation of raw data files, library spectrumfiles or results files. This standard format has the extension“.cdf” (derived from NetCDF). The contents of the file includetypical header information like instrument, sample, and acqui-sition method description, followed by raw, library or
5、pro-cessed data. Once data have been written or converted to thisprotocol, they can be read and processed by software packagesthat support the protocol.1.3 This specification does not provide for the storage ofdata acquired simultaneous to and integrated with the massspectrometric data, but on other
6、 detectors; for example at-tached to the mass spectrometers liquid or gas chromato-graphic system. Related Specification E1947 and Guide1948E1948 describe the storage of 2-dimensional chromato-graphic data.1.4 The software transfer vehicle used for the protocol inthis specification is NetCDF, which
7、was developed by theUnidata Program and is funded by the Division ofAtmosphericSciences of the National Science Foundation.21.5 The protocol in this specification is intended to (1)transfer data between various vendors instrument systems, (2)provide Laboratory Information Management Systems (LIMS)co
8、mmunications, (3) link data to document processing appli-cations, (4) link data to spreadsheet applications, and (5)archive analytical data, or a combination thereof. The protocolis a consistent, vendor independent data format that facilitatesthe analytical data interchange for these activities.1.6
9、The protocol consists of:1.6.1 This specification on mass spectrometric data, whichgives the full definitions for each one of the generic massspectrometric data elements used in implementation of theprotocol. It defines the analytical information categories, whichare a convenient way for sorting ana
10、lytical data elements tomake them easier to standardize.1.6.2 Guide E2078 on mass spectrometric data, which givesthe full details on how to implement the content of the protocolusing the public-domain NetCDF data interchange system. Itincludes a brief introduction to using NetCDF and describes anAPI
11、 (Application Programming Interface) that is intended to beincorporated into application programs to read or writeNetCDF files. It is intended for software implementors, notthose wanting to understand the definitions of data in a massspectrometric dataset.1.6.3 NetCDF Users Guide.2. Referenced Docum
12、ents2.1 ASTM Standards:3E2078 Guide for Analytical Data Interchange Protocol forMass Spectrometric DataE1947 Specification for Analytical Data Interchange Proto-col for Chromatographic DataE1948 Guide for Analytical Data Interchange Protocol forChromatographic Data2.2 Other Standards:NetCDF Users Gu
13、ide41This specification is under the jurisdiction of ASTM Committee E13 onMolecular Spectroscopy and Separation Science and is the direct responsibility ofSubcommittee E13.15 on Analytical Data.Current edition approved Nov. 1, 2010. Published November 2010. Originallyapproved in 2000. Last previous
14、edition approved in 2005 as E2077 00 (2005).DOI: 10.1520/E2077-00R10.2For more information on the NetCDF standard, contact Unidata at www.uni-data.ucar.edu.3For referenced ASTM standards, visit the ASTM website, www.astm.org, orcontact ASTM Customer Service at serviceastm.org. For Annual Book of AST
15、MStandards volume information, refer to the standards Document Summary page onthe ASTM website.4Available from Russell K. Rew, Unidata Program Center, University Corpora-tion for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307-3000.1Copyright ASTM International, 100 Barr Harbor Drive, PO Box
16、C700, West Conshohocken, PA 19428-2959, United States.Occupational Safety and Health Administration (OSHA)Standards-29 CFR part 19105IEEE 4886IEEE -8026EIA - 23272.3 ISO Standards:88601:1988 Data elements and interchange formats (Firstedition published 1988-06-15; with Technical Corrigen-dum 1 publi
17、shed 1991-05-01)639: 1988 Code for the representation of names of lan-guages9000 Quality Management SystemsISO/IEC - 88023. Terminology3.1 Analytical Information ClassesThe Mass Spectrom-etry Information Model categorizes mass spectrometric infor-mation into a number of information “classes.” There
18、is not adirect mapping of these classes into the implementation cat-egories described further below. The implementation catego-ries describe the information hierarchy; the classes describe thecontents within the hierarchy. The model presented here onlypartially addresses these classes. In particular
19、, the last two(Processed Results and Component Quantitation Results) arenot described at all. Only Implementation Category 1 isrequired for compliance within this specification. Informationabout the other implementation categories is provided forhistorical interest. The classes defined here are:3.1.
20、1 Administrativeinformation for administrative track-ing of experiments.3.1.2 Instrument-IDinformation about the instrument thatgenerally does not change from experiment to experiment.3.1.3 Sample Descriptioninformation describing thesample and its history, handling and processing.3.1.4 Test Methoda
21、ll information used to generate the rawdata and processed results. This includes instrument control,detection, calibration, data processing and quantitation meth-ods.3.1.5 Raw Datathe data as stored in the data file, alongwith any parameters needed to describe it.3.1.6 Processed Resultsprocessing in
22、formation and val-ues derived from the raw data.3.1.7 Component Quantitation Resultsindividual quanti-tation results for components in a complex mixture.3.2 Definitions for Administrative Information ClassThese definitions are for those data elements that are imple-mented in the protocol. See Table
23、1.TABLE 1 Administrative Information ClassNOTE 1Particular analytical information categories (C1, C2, C3, C4,or C5) are assigned to each data element under the Category column. Themeaning of this category assignment is explained in Section 5.NOTE 2The Required column indicates whether a data element
24、 isrequired, and if required, for which categories. For example, M1234indicates that that particular data element is required for any dataset thatincludes information from Category 1, 2, 3, or 4. M4 indicates that a dataelement is only required for Category 4 datasets.NOTE 3Unless otherwise specifie
25、d, data elements are generally re-corded to be their actual test values, instead of the nominal values thatwere used at the initiation of a test.NOTE 4A table is not to be interpreted as a table of keywords. Thesoftware implementation is independent of the data element names usedhere, and is in fact
26、 quite different. Likewise, the datatypes given are not animplementation representation, but a description of the form of the dataelement name. That is, a data element labeled as floating point may, forexample, be implemented as a double precision floating point number; inthis document, it is suffic
27、ient to note it as floating point without referenceto precision.Data Element Name Datatype Category Requireddataset-completeness string C1 M12345protocol-template-revision string C1 M12345netcdf-revision string C1 M12345languages string C1 or C5 . . .administrative-comments string C1 or C2 . . .data
28、set-origin string C1 M4dataset-owner string C1 . . .dataset-date-time-stamp string C1 M1234injection-date-time-stamp string C1 M1234experiment-title string C1 . . .experiment-cross-references string arrayn C3 or C4operator-name string C1 M4experiment-type string C1 or C4 . . .pre-experiment-program-
29、name string C2 or C5 . . .post-experiment-program-name string C2 or C5 . . .number-of-times-processed integer C5number-of-times-calibrated integer C5calibration-history string arrayn C5source-file-reference string C5 M4source-file-format string C5source-file-date-time-stamp string C5 M4external-file
30、-references string arrayn C5error-log string C53.2.1 administrative-commentscomments about thedataset identification of the experiment. This free text field isfor anything in this information class that is not covered by theother data elements in this class.3.2.2 calibration-historyan audit trail of
31、 file names anddata sets which records the calibration history; used for GoodLaboratory Practice (GLP) compliance.3.2.3 dataset-completenessindicates which analytical in-formation categories are contained in the dataset. The stringshould exactly list the category values, as appropriate, as one ormor
32、e of the following “C1+C2+C3+C4+C5,” in a stringseparated by plus (+) signs. This data element is used to checkfor completeness of the analytical dataset being transferred.3.2.4 dataset-date-time-stampindicates the absolute timeof dataset creation relative to Greenwich Mean Time. Ex-pressed as the s
33、ynthetic datetime given in the form:YYYYMMDDhhmmss6ffff.3.2.4.1 DiscussionThis is a synthesis of ISO 8601, whichcompensates for local time variations.3.2.4.2 DiscussionThe YYYYMMDDhhmmss expressesthe local time, and time differential factor (ffff) expresses the5E13Available from Occupational Safety
34、and Health Administration (OSHA),200 Constitution Ave., NW, Washington, DC 20210.6Available from Institute of Electrical and Electronics Engineers, Inc. (IEEE),445 Hoes Ln., P.O. Box 1331, Piscataway, NJ 08854-1331.7Available from Electronic Industries Alliance (EIA), 2500 Wilson Blvd.,Arlington, VA
35、 22201.8Available from ISO, 1 Rue de Varembe, Case Postale 56, CH 1211, Geneve,Switzerland.E2077 00 (2010)2hours and minutes between local time and the CoordinatedUniversal Time (UTC or Greenwich Mean Time, as dissemi-nated by time signals), as defined in ISO 8601. The timedifferential factor (ffff)
36、 is represented by a four-digit numberpreceded by a plus (+) or a minus () sign, indicating thenumber of hours and minutes that local time differs from theUTC. Local times vary throughout the world from UTC by asmuch as 1200 h (west of the Greenwich Meridian) and by asmuch as +1300 h (east of the Gr
37、eenwich Meridian). When thetime differential factor equals zero, this indicates a zero hour,zero minute, and zero second difference from Greenwich MeanTime.3.2.4.3 DiscussionAn example of a value for a datetimewould be: 1991,08,01,12:30:23-0500 or 19910801123023-0500. In human terms this is 23 s pas
38、t 12:30 PM on August 1,1991 in New York City. Note that the 0500 h is 5 full hourstime behind Greenwich Mean Time. The ISO standard permitsthe use of separators as shown, if they are required to facilitatehuman understanding. However, separators are not requiredand consequently shall not be used to
39、separate date and time forinterchange among data processing systems.3.2.4.4 DiscussionThe numerical value for the month ofthe year is used, because this eliminates problems with thedifferent month abbreviations used in different human lan-guages.3.2.5 dataset-originname of the organization, address,
40、telephone number, electronic mail nodes, and names of indi-vidual contributors, including operator(s), and any other infor-mation as appropriate. This is where the dataset originated.3.2.6 dataset-ownername of the owner of a proprietarydataset. The person or organization named here is responsiblefor
41、 this fields accuracy. Copyrighted data should be indicatedhere.3.2.7 error-loginformation that serves as a log for failuresof any type, such as instrument control, data acquisition, dataprocessing or others.3.2.8 experiment-cross-referencesan array of stringswhich reference other related experiment
42、s.3.2.9 experiment-titleuser-readable, meaningful name forthe experiment or test that is given by the scientist.3.2.10 experiment-typename of the type of data stored inthis file. Select one of the types in the following list.3.2.10.1 DiscussionThe valid types are:centroided mass spectruma data set c
43、ontaining centroided singleor multiple scan mass spectra. This includes selected ion monitoring/recording (SIM/SIR) data, represented as mass-intensity pairs. This isthe default.continuum mass spectruma data set containing single or multiplescan mass spectra in continuum (non-centroided or profile)
44、form. Scansare represented as mass-intensity pairs, whether incrementally spacedor not.library mass spectruma data set consisting of one or more spectraderived from a spectral library. This is distinguished from an experi-mental mass spectral data set in that each spectrum in the library set hasasso
45、ciated chemical identification and other information.3.2.10.2 DiscussionA required Raw Data Informationparameter, the number of scans, is used to define the shape ofthe data in the file, that is, to differentiate between single andmultiple spectrum files.Another parameter, the scan number, isused to
46、 determine whether multiple scan files have an order orrelatedness between scans.3.2.10.3 DiscussionSome instruments are capable ofmixed mode data acquisition, for example, alternating positive/negative EI (Electron Ionisation) or CI (Chemical Ionisation)scans. In order to keep this interchange stan
47、dard as simple aspossible, each scan mode must be treated as a separate dataset regardless of how the data are actually stored in the sourcedata file. Alternating positive/negative EI data, for example,will generate two interchange files (possibly simultaneously,depending on the implementation); one
48、 for the positive EIscans and one for the negative EI scans. These files may bemade mutually cross-referential using their “external-file-references” fields.3.2.11 external-file-referencesan array of strings listingfile names referred to from within the raw data file.These couldinclude, for example,
49、 tune parameter, method, calibration,reference, sequence, or other files. NetCDF files produced inparallel (such as paired files containing alternating EI/CI scans)should be cross-referenced here.3.2.12 injection-date-time-stampindicates the absolutetime of sample injection relative to Greenwich Mean Time.Expressed as the synthetic datetime given in the form:YYYYMMDDhhmmss 6ffff. See dataset-date-time-stamp fordetails of the ISO standard definition of a date-time-stamp.3.2.13 languagesoptional list of natural (human) lan-guages and pr
