MassBank Consortium (May 13, 2022)
- May 2022: With version 2.6.0 MassBank introduces a new ACCESSION scheme. It offers more freedom for contributors in the naming of their records. The new scheme consists of three fields separated by 'minus' signs and follows the format ID-[A-Z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. Now it can be up to 32 characters long and is comprised of letters, digits and the '' sign. The third field is the ID assigned by the contributor and can be up to 64 characters long and is also comprised of letters, digits and the '' sign.
- April 2022: Added EAD (Electron Activated Dissocation) as allowed fragmentation mode.
- July 2021: Move to a semantic versioning scheme X.Y.Z with Z increases for changes in the description or fixing of typos, Y increases for changes that also change the Validator software and X increases with changes that break compatibility with older versions of the software.
- March 2020: Add new tag for the inlet type.
- October 2019: Add UVPD dissociation method and some undocumented or new tags.
- September 2018: Add a new PROJECT tag, some undocumented tags used in RMassBank (COMMENT: CONFIDENCE, COMMENT: INTERNAL_ID, AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE, AC$MASS_SPECTROMETRY: RESOLUTION, MS$DATA_PROCESSING: REANALYZE, MS$DATA_PROCESSING: RECALIBRATION) and cross references to HUPO-PSI
- July 2017: CH$CDK_DEPICT added to render partially defined structures with CDK depict. AC$CHROMATOGRAPHY: NAPS_RTI added to provide relative retention time information.
- June 2017: CH$LINK: COMPTOX added to link the CompTox Chemistry Dashboard
- March 2016: The default Creative Commons license of MassBank record is defined as CC BY. Two new tags are added, CH$LINK: INCHIKEY and PK$SPLASH. InChI key in CH$LINK: INCHIKEY is a hashed version of InChI code and used as an optional, common link based on chemical structures. SPLASH in PK$SPLASH (Section 2.6.1) is a mandatory, hashed identifier of mass spectra.
Each MassBank Record has one-to-one relation to a specific mass spectrum. It is assumed that the sample of measurement of each mass spectrum is a single chemical substance. MassBank Record Information is classified into single line information and multiple line information, mandatory and optional, unique and iterative.
Single line information is either one of the followings:
tag : space value (; space value)tag : space subtag space value (; space value)
Multiple line information:
- First line:
tag: space - Following lines:
space space value
Last line of a MassBank Record is //.
General format is [CV label, accession, name, value]. Any field that is not available MUST be left empty. Should the name contain commas, quotes MUST be added to avoid problems with parsing.
Example:
[CV label, accession, name, value]
[MS, MS:1000443, Mass Analyzer Type, Orbitrap]
[MS, MS:1001477, SpectraST,]
[label, accession, “first part of the param name, second part of the name”, value]
MassBank Record Information in a MassBank Record is arranged in a fixed order (see Section 2).
| Tag | Mandatory/ Optional |
Unique/ Iterative |
Single line/ Multiple line |
Description | Subsection in manual |
|---|---|---|---|---|---|
| Record Specific Information | |||||
| ACCESSION | M | U | S | Record identifier | 2.1.1 |
| RECORD_TITLE | M | U | S | Short title of the record | 2.1.2 |
| DATE | M | U | S | Date of creation or last modification of record | 2.1.3 |
| AUTHORS | M | U | S | Name and affiliation of authors | 2.1.4 |
| LICENSE | M | U | S | Creative Commons License or its compatible terms | 2.1.5 |
| COPYRIGHT | O | U | S | Copyright | 2.1.6 |
| PUBLICATION | O | U | S | Bibliographic information of reference | 2.1.7 |
| PROJECT | O | U | S | Information on a related project) | 2.1.8 |
| COMMENT | O | I | S | Comments | 2.1.9 |
| Information of Chemical Compound Analyzed | |||||
| CH$NAME | M | I | S | Chemical name | 2.2.1 |
| CH$COMPOUND_CLASS | M | U | S | Chemical category | 2.2.2 |
| CH$FORMULA | M | U | S | Chemical formula | 2.2.3 |
| CH$EXACT_MASS | M | U | S | Exact mass | 2.2.4 |
| CH$SMILES | M | U | S | SMILES code | 2.2.5 |
| CH$IUPAC | M | U | S | InChI code | 2.2.6 |
| CH$LINK subtag identifier | O | I | S | External database name with identifier | 2.2.8 |
| Information of Biological Sample | |||||
| SP$SCIENTIFIC_NAME | O | U | S | Scientific name of biological species | 2.3.1 |
| SP$LINEAGE | O | U | S | Lineage of species | 2.3.2 |
| SP$LINK subtag identifier | O | I | S | External database name with identifier | 2.3.3 |
| SP$SAMPLE | O | I | S | Information of sample preparation | 2.3.4 |
| Analytical Methods and Conditions | |||||
| AC$INSTRUMENT | M | U | S | Commercial name and manufacturer of instrument | 2.4.1 |
| AC$INSTRUMENT_TYPE | M | U | S | Type of instrument | 2.4.2 |
| AC$MASS_SPECTROMETRY: MS_TYPE | M | U | S | MSn type of data | 2.4.3 |
| AC$MASS_SPECTROMETRY: ION_MODE | M | U | S | Positive or negative mode of ion detection | 2.4.4 |
| AC$MASS_SPECTROMETRY: subtag | O | U | S | Analytical conditions of mass spectrometry | 2.4.5 |
| AC$CHROMATOGRAPHY: subtag | O | U/I | S | Analytical conditions of chromatographic separation | 2.4.6 |
| AC$GENERAL: subtag | O | U/I | S | General analytical conditions and information | 2.4.7 |
| Description of mass spectral data | |||||
| MS$FOCUSED_ION: subtag | O | U | S | Precursor ion and m/z | 2.5.1 |
| MS$DATA_PROCESSING: subtag | O | U | S | DATA processing method | 2.5.2 |
| Peak Information | |||||
| PK$SPLASH | M | U | S | Hashed identifier of mass spectra | 2.6.1 |
| PK$ANNOTATION | O | U | M | Chemical annotation of peaks by molecular formula | 2.6.2 |
| PK$NUM_PEAK | M | U | S | Total number of peaks | 2.6.3 |
| PK$PEAK | M | U | M | Peak(m/z, intensity and relative intensity | 2.6.4 |
| Supplementary Definitions | |||||
| Description of isotope-labeled chemical compound | 2.7.1 | ||||
- General note. Decimal point should be a period,
., but not a comma,,. For example,m/z 425.7. No thousand separator is inserted.
- Table 1 summarizes the current MassBank Record Information.
- MassBank Record Information consists of 6 groups (Table 2).
| Information groups | Sections |
|---|---|
| Record Specific Information | 2.1 |
| Chemical Information (Tag starts with CH$) | 2.2 |
| Sample Information (Tag starts with SP$) | 2.3 |
| Analytical Chemistry Information (Tag starts with AC$) | 2.4 |
| Mass Spectral Data Information (Tag starts with MS$) | 2.5 |
| Mass Spectral Peak Data (Tag starts with PK$) | 2.6 |
- Information should be arranged by the order shown in Table 2.
Identifier of the MassBank Record. Mandatory
Example:
ACCESSION: MSBNK-AAFC-AC000101
The MassBank accession consists of three fields separated by - signs and follows the format ID-[A-Za-z0–9_]{1,32}-[A-Z0–9_]{1,64}. The field ID will always be MSBNK for official MassBank releases. The second field is the contributor ID and is usually assigned by MassBank staff. It can be up to 32 characters long and is comprised of letters, digits and the _ sign. The third field is the ID assigned by the contributor and an be up to 64 characters long and is comprised of capital letters, digits and the _ sign.
The list of List of contributors and projects is maintained at https://github.com/MassBank/MassBank-data/blob/master/List_of_Contributors_Prefixes_and_Projects.md.
A deprecated record is marked with the tag DEPRECATED: followed by date and reason on the second line. The content of a deprecated record may not be valid.
Example:
ACCESSION: MSBNK-ISAS_Dortmund-IA000311
DEPRECATED: 2019-11-25 Wrong MS measurement assigned
Brief Description of MassBank Record. Mandatory
Example:
RECORD_TITLE: (-)-Nicotine; ESI-QQ; MS2; CE 40 V; [M+H]+
It consists of the values of CH$NAME; AC$INSTRUMENT_TYPE; AC$MASS_SPECTROMETRY: MS_TYPE.
Date of the Creation or the Last Modification of MassBank Record. Mandatory
Example:
DATE: 2011.02.21 (Created 2007.07.07)
Authors and Affiliations of MassBank Record. Mandatory
Example:
AUTHORS: Akimoto N, Grad Sch Pharm Sci, Kyoto Univ and Maoka T, Res Inst Prod Dev.
If appropriate, it is suggested (but not mandatory) to add MARC relator terms after names to clarify the contributions of different authors. In particular, the following tags are suggested:
[dtc]: Data contributor, i.e. the person(s) who contribute the data, e.g. who acquired the raw data in-house, or who deposited data files that serve as the basis for the record in a public repository. This person or entity is not necessarily involved in the creation of the record.[com]: Compiler, i.e. the person who created the record (but did not necessarily acquire the data or has any other scientific involvement).
Example:
AUTHORS: Earll M, EMBL-EBI [dtc]; Beisken S, EMBL-EBI [dtc]; Stravs MA, Eawag [com]
Creative Commons License of Re-use of MassBank Record. Mandatory
Example:
LICENSE: CC BY
Contributors to MassBank are encouraged to show the license CC BY. This license mean that others are free to "share" (copy and redistribute the MassBank record in any medium or format) and to "adapt" (remix, transform, and build upon the MassBank record) for any purpose, even commercially. The contributors cannot revoke these freedoms as long as the others follow the license terms.
Allowed licenses are: CC0, CC BY, CC BY-NC, CC BY-NC-SA, CC BY-SA check https://creativecommons.org/licenses/
Copyright of MassBank Record. Optional
Example:
COPYRIGHT: Keio University
Reference of the Mass Spectral Data. Optional
Example 1:
PUBLICATION: Iida T, Tamura T, et al, J Lipid Res. 29, 165-71 (1988). [PMID: 3367086]
Example 2:
PUBLICATION: Schymanski EL, Jeon J, et al., Environ. Sci. Technol. 48, 2097-2098 (2014). [DOI: 10.1021/es5002105]
Citation with PubMed ID or DOI is recommended.
A project tag of a project related to the record. Optional Project tags currently used are listed in the “Project Tag” column of the MassBank List of contributors, prefixes and projects.
Example:
PROJECT: NATOXAQ Natural Toxins and Drinking Water Quality - From Source to Tap
PROJECT: SOLUTIONS for present and future emerging pollutants in land and water resources management
Comments. Optional and Iterative
In MassBank, COMMENT fields are often used to show the relations of the present record with other MassBank records and with data files. In these cases, the terms in brackets [ and ] are reserved for the comments specific to the following five examples. Example 1:
COMMENT: This record is a MS3 spectrum. Link to the MS2 spectrum is added in the following comment field.
COMMENT: [MS2] KO008089
Example 2:
COMMENT: This record was generated by merging the following three MassBank records.
COMMENT: [Merging] KO006229 Tiglate; ESI-QTOF; MS2; CE:10 V [M-H]-.
COMMENT: [Merging] KO006230 Tiglate; ESI-QTOF; MS2; CE:20 V [M-H]-.
COMMENT: [Merging] KO006231 Tiglate; ESI-QTOF; MS2; CE:30 V [M-H]-.
Example 3:
COMMENT: This record was merged into a MassBank record, KOX00012, with other records.
COMMENT: [Merged] KOX00012
Example 4:
COMMENT: Analytical conditions of LC-MS were described in separate files.
COMMENT: [Mass spectrometry] ms1.txt
COMMENT: [Chromatography] lc1.txt.
Example 5:
COMMENT: Profile spectrum of this record is given as a JPEG file.
COMMENT: [Profile] CA000185.jpg
Comment subtags. Optional and Iterative
Description of a confidence level (e.g. Reference Standard or Standard Compound) and/or the confidence according to Schymanski et al. 2014
Example:
COMMENT: CONFIDENCE Reference Standard (Level 1)
Internal ID tag of the laboratory (e.g. compound number).
Example:
COMMENT: INTERNAL_ID 21
Name of the Chemical Compound Analyzed. Mandatory and Iterative
Example:
CH$NAME: D-Tartaric acid
CH$NAME: (2S,3S)-Tartaric acid
No prosthetic molecule of adducts (HCl, H2SO3, H2O, etc), conjugate ions (Chloride, etc) , and protecting groups (TMS, etc.) is included. Synonyms could be added. If chemical compound is a stereoisomer, stereochemistry should be indicated.
Category of Chemical Compound. Mandatory
Example:
CH$COMPOUND_CLASS: Natural Product; Carotenoid; Terpenoid; Lipid
Either Natural Product or Non-Natural Product should be precedes the other class names .
Molecular Formula of Chemical Compound. Mandatory
Example 1:
CH$FORMULA: C9H10ClNO3
Example 2:
CH$FORMULA: [C5H14NO]+
It follows the Hill's System. No prosthetic molecule is included (see 2.2.1 CH$NAME). If possible the neutral form of a functional group should be given. Charged molecules are given in square brackets with charge behind. Molecular formulae of derivatives by chemical modification with TMS, etc. should be given in 2.5.1 MS$FOCUSED_ION: DERIVATIVE_FORM.
Monoisotopic Mass of Chemical Compound. Mandatory
Example:
CH$EXACT_MASS: 430.38108
A value with 5 digits after the decimal point is recommended.
SMILES String. Mandatory
Example:
CH$SMILES: NCC(O)=O
Isomeric SMILES but not a canonical one.
IUPAC International Chemical Identifier (InChI Code). Mandatory
Example:
CH$IUPAC: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
Not IUPAC name.
Displays partially defined structures with CDK depict in record view. In test phase, advanced users only. Optional and Iterative
Example 1:
CH$CDK_DEPICT_SMILES CCOCCOCCO |Sg:n:3,4,5:2:ht| PEG-2
Example 2:
CH$CDK_DEPICT_GENERIC_SMILES c1ccc(cc1)/C=C/C(=O)O[R]
Example 2:
CH$CDK_DEPICT_STRUCTURE_SMILES c1ccc(cc1)/C=C/C(=O)O
Identifier and Link of Chemical Compound to External Databases. Optional and Iterative
Example:
CH$LINK: CAS 56-40-6
CH$LINK: COMPTOX DTXSID50274017
CH$LINK: INCHIKEY UFFBMTHBGFGIHF-UHFFFAOYSA-N
CH$LINK: KEGG C00037
CH$LINK: PUBCHEM SID: 11916 CID:182232
Currently MassBank records have links to the following external databases:
CAS
CAYMAN
CHEBI
CHEMBL
CHEMPDB
CHEMSPIDER
COMPTOX
HMDB
INCHIKEY
KAPPAVIEW
KEGG
KNAPSACK
LIPIDBANK
LIPIDMAPS
NIKKAJI
PUBCHEM
ZINC
CH$LINK fields should be arranged by the alphabetical order of database names.
Scientific Name of biological species, from which the sample was prepared. Optional
Example:
SP$SCIENTIFIC_NAME: Mus musculus
Evolutionary lineage of the species, from which the sample was prepared. Optional
Example:
SP$LINEAGE: cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus
Identifier of Biological Species in External Databases. Optional and iterative
Example:
SP$LINK: NCBI-TAXONOMY 10090
SP$LINK fields should be arranged by the alphabetical order of database names.
Tissue or Cell, from which Sample was Prepared. Optional and iterative
Example:
SP$SAMPLE: Liver extracts
Commercial Name and Model of Chromatographic Separation Instrument, if any were coupled, and Mass Spectrometer and Manufacturer. Mandatory
Example:
AC$INSTRUMENT: LC-10ADVPmicro HPLC, Shimadzu; LTQ Orbitrap, Thermo Electron.
Cross-reference to HUPO-PSI: Instrument model [MS:1000031] All the instruments are given together in a single line. This record is not iterative.
General Type of Instrument. Mandatory
Example:
AC$INSTRUMENT_TYPE: LC-ESI-QTOF
Format is (Separation tool type-)Ionization method-Ion analyzer type(Ion analyzer type).
Separation tool types are:
CE
GC
LC
Ionization methods are:
APCI
APPI
EI
ESI
FAB
MALDI
FD
CI
FI
SIMS
Ion analyzer types are:
B
E
FT
IT
Q
TOF
In tandem mass analyzers, no - is inserted between ion analyzers.
FT includes FTICR and other type analyzers using FT, such as Orbitrap(R). IT comprises quadrupole ion trap analyzers such as 3D ion trap and linear ion trap.
Other examples of AC$INSTRUMENT_TYPE data are:
ESI-QQ
ESI-QTOF
GC-EI-EB
LC-ESI-ITFT
Cross-reference to HUPO-PSI: Ionization methods [MS:1000008]: APCI[MS:1000070], APPI[MS:1000382], EI[MS:1000389], ESI[MS:1000073], FAB[MS:1000074], MALDI[MS:1000075], FD[MS:1000257], CI[MS:1000071], FI[MS:1000258], SI[MS:1000402].
Ion analyzer types [MS:1000443]: B[MS:1000080], E[MS:1000254], IT[MS:1000264], Q[MS:1000081], TOF[MS:1000084]
Data Type. Mandatory
Example:
AC$MASS_SPECTROMETRY: MS_TYPE MS2
Other examples of AC$MASS_SPECTROMETRY data are as follows:
MS
MS2
MS3
MS4
MS5
MSn
Brief definition of terms used in MS_TYPE:
MS- MS1 spectrum(MS:1000579)MS2- MSn spectrum(MS:1000580) with ms level(MS:1000511) = 2MS3- MSn spectrum(MS:1000580) with ms level(MS:1000511) = 3MSn- use for any other multi stage acquisition method, which does not fit in the above scheme, like merged MS spectra from different stages
Polarity of Ion Detection. Mandatory
Example:
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
Either of POSITIVE or NEGATIVE is allowed. Cross-reference to HUPO-PSI: POSITIVE [MS, MS:1000130, positive scan,] or NEGATIVE [MS:1000129, negative scan,]; ION_MODE [MS, MS:1000465, scan polarity,]
Other Optional Experimental Methods and Conditions of Mass Spectrometry.
Description is a list of numerical values with/without unit or a sentence.
AC$MASS_SPECTROMETRY fields should be arranged by the alphabetical order of subtag names.
Voltage Applied to Capillary Electrophoresis or Voltage Applied to the Interface of LC-MS in kV.
Example:
AC$MASS_SPECTROMETRY: CAPILLARY_VOLTAGE 4 kV
Collision Energy for Dissociation.
Example 1:
AC$MASS_SPECTROMETRY: COLLISION_ENERGY 20 kV
Example 2:
AC$MASS_SPECTROMETRY: COLLISION_ENERGY Ramp 10-50 kV
Example 3:
AC$MASS_SPECTROMETRY: COLLISION_ENERGY 10% (nominal)
Name of Collision Gas.
Example:
AC$MASS_SPECTROMETRY: COLLISION_GAS N2
Cross-reference to HUPO-PSI: Collision gas [MS:1000419]
Date of Analysis.
Flow Rate of Desolvation Gas.
Example:
AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 600.0 L/h
Temperature of Desolvation Gas.
Example:
AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 400 C
Fragmentation method used for dissociation or fragmentation.
Example:
AC$MASS_SPECTROMETRY: FRAGMENTATION_MODE CID
Data of type AC$FRAGMENTATION_MODE are:
BIRD
CID
ECD
EDD
ETD
HCD
IRMPD
MPD
NETD
SID
UVPD
EAD
Cross-reference to HUPO-PSI: dissociation method [MS:1000044]
The method by which gas phase ions are generated from the sample.
Example:
AC$MASS_SPECTROMETRY: IONIZATION ESI
Ionization methods are:
APCI
APPI
EI
ESI
FAB
MALDI
FD
CI
FI
SIMS
Cross-reference to HUPO-PSI: ionization type [MS:1000008]
Energy of Ionization (aka FRAGMENT_VOLTAGE, IONIZATION_POTENTIAL).
Example:
AC$MASS_SPECTROMETRY: IONIZATION_ENERGY 70 eV
Desorption and Ionization Conditions in MALDI.
Example:
AC$MASS_SPECTROMETRY: LASER 337 nm nitrogen laser, 20 Hz, 10 nsec
Matrix Used in MALDI and FAB.
Example:
AC$MASS_SPECTROMETRY: MATRIX 1-2 uL m-NBA
Relative Mass Accuracy.
Example:
AC$MASS_SPECTROMETRY: MASS_ACCURACY 50 ppm over a range of about m/z 100-1000
Mass Range of the Scan (aka Scanning Range or Scan Range) in m/z. The m/z is given as an integer. The data could be extracted of the raw data automatically. If derived of existing data, decimals must be converted to the next lower integer in the case of the lower limit (e.g., 10.49 -> 10). In case of the upper limit, the m/z is converted to next larger integer (e.g. 10.49 -> 11).
Example:
AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z 100-1000
Name of Reagent Gas.
Example:
AC$MASS_SPECTROMETRY: REAGENT_GAS ammonia
Resolution (aka Mass Resolution or Resolving Power) is the smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
Example:
AC$MASS_SPECTROMETRY: RESOLUTION 15000
Cross-reference to HUPO-PSI: mass resolution [MS:1000011]
Setting of the Scan Event without Range which should be given in 2.4.5 AC$MASS_SPECTROMETRY: MASS_RANGE_M/Z.
Example 1:
AC$MASS_SPECTROMETRY: SCANNING_SETTING 1 sec/scan
Example 2:
AC$MASS_SPECTROMETRY: SCANNING_SETTING 1 amu/sec
Example 3:
AC$MASS_SPECTROMETRY: SCANNING_SETTING 1 cycle/sec
Temperature of the Ion Source in GC-MS and LC-MS (aka Ion Source Temperature), for Example of the EI Source or the Heated ESI Source.
Example:
AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE 280 C
ACTIVATION_PARAMETER
ACTIVATION_TIME
ATOM_GUN_CURRENT
AUTOMATIC_GAIN_CONTROL
BOMBARDMENT
CAPILLARY_TEMPERATURE
CAPILLARY_VOLTAGE
CDL_SIDE_OCTOPOLES_BIAS_VOLTAGE
CDL_TEMPERATURE
DATAFORMAT
DRY_GAS_FLOW
DRY_GAS_TEMP
GAS_PRESSURE
HELIUM_FLOW
INTERFACE_VOLTAGE
ION_GUIDE_PEAK_VOLTAGE
ION_GUIDE_VOLTAGE
ION_SPRAY_VOLTAGE
IT_SIDE_OCTOPOLES_BIAS_VOLTAGE
LENS_VOLTAGE
NEBULIZER
NEBULIZING_GAS
NEEDLE_VOLTAGE
OCTPOLE_VOLTAGE
ORIFICE_TEMP
ORIFICE_TEMPERATURE
ORIFICE_VOLTAGE
PROBE_TIP
RING_VOLTAGE
SAMPLE_DRIPPING
SKIMMER_VOLTAGE
SPRAY_VOLTAGE
TUBE_LENS_VOLTAGE
Experimental Methods and Conditions of Chromatographic Separation. Optional
AC$CHROMATOGRAPHY fields should be arranged by the alphabetical order of subtag names.
Carrier Gas Used for GC-MS.
Example 1:
AC$CHROMATOGRAPHY: CARRIER_GAS Helium
Example 2:
AC$CHROMATOGRAPHY: CARRIER_GAS Nitrogen
Example 3:
AC$CHROMATOGRAPHY: CARRIER_GAS Hydrogen
Commercial Name of Chromatography Column and Manufacture.
Example of LC Column Name:
AC$CHROMATOGRAPHY: COLUMN_NAME Acquity UPLC BEH C18 2.1 by 50 mm (Waters, Milford, MA, USA)
Example of GC Column Name:
AC$CHROMATOGRAPHY: COLUMN_NAME Fused silica capillary id=50 um L=100 cm (HMT, Tsuruoka, Japan)
Static Column Temperature in GC-MS and LC-MS.
Example:
AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C
Dynamic Column Temperature Gradient (aka Oven Temperature) in GC-MS and LC-MS.
Example:
AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE_GRADIENT 55 C at 0 min, 55 C at 3 min, 180 C at 11.33 min, 280 C at 26.72 min, 280 C at 31.72 min, 300 C at 33.72 min, 300 C at 39 min
Gradient of Mobile Phases in LC-MS.
Example:
AC$CHROMATOGRAPHY: FLOW_GRADIENT 0/100 at 0 min, 15/85 at 5 min, 21/79 at 20 min, 90/10 at 24 min, 95/5 at 26 min, 0/100, 30 min
Flow Rate of Migration Phase in GC-MS and LC-MS.
Example:
AC$CHROMATOGRAPHY: FLOW_RATE 0.25 mL/min
Temperature of the Injection Port in GC-MS.
Example:
AC$CHROMATOGRAPHY: INJECTION_TEMPERATURE 250 C
Temperature of the Injection Port in GC-MS in Case of Cold Injection, Thermodesorption or other Trapping Systems.
Example:
AC$CHROMATOGRAPHY: INJECTION_TEMPERATURE_GRADIENT 10 C at 0 sec, 250 C at 3 sec with 80 C/sec
Type of the Injection or of the Injection Port
Example:
AC$CHROMATOGRAPHY: INLET_TYPE flow injection analysis
Data of type AC$CHROMATOGRAPHY: INLET_TYPE are:
atmospheric pressure inlet
capillary flow technology
cold injection inlet
cold on column inlet
direct inlet
direct insertion probe
direct liquid introduction
electrospray inlet
flow injection analysis
infusion
nanospray inlet
split inlet
splitless inlet
Cross-reference to HUPO-PSI: inlet type [MS:1000007]
C8-C30 n-Alkanes Based Retention Time Index for GC-MS.
Example:
AC$CHROMATOGRAPHY: KOVATS_RTI 2000
Reference: E. Kovats, Adv. Chromatogr. 1 (1965) 229 Reference: E. Kovats, Helv. Chim. Acta 41 (1958) 1915 Reference: Rostad et al. 1986
Polycyclic Aromatic Hydrocarbons Based Retention Time Index for GC-MS.
Example:
AC$CHROMATOGRAPHY: LEE_RTI 200
Reference: Rostad et al. 1986
N-alkylpyrinium-3-sulfonate Based Retention Time Index for LC-MS.
Example:
AC$CHROMATOGRAPHY: NAPS_RTI 100
Reference: Quilliam et al. 2015
Experimental Retention Time Index (Range 1-1000) for LC-MS based on the QSRR Approach of University of Athens, Trace Analysis and Mass Spectrometry Group.
Example:
AC$CHROMATOGRAPHY: UOA_RTI 50
Reference: Aalizadeh et al. 2019
Predicted Retention Time Index (Range 1-1000) for LC-MS based on the QSRR Approach of University of Athens, Trace Analysis and Mass Spectrometry Group.
Example:
AC$CHROMATOGRAPHY: UOA_PREDICTED_RTI 50
Reference: Aalizadeh et al. 2019
Experimental Retention Time based on Chromatography.
Example:
AC$CHROMATOGRAPHY: RETENTION_TIME 40.3 min
Cross-reference to HUPO-PSI: Retention time [MS:1000016]
Predicted Retention Time for LC-MS based on the QSRR Approach of University of Athens, Trace Analysis and Mass Spectrometry Group.
Example:
AC$CHROMATOGRAPHY: TRAMS_PREDICTED_RETENTION_TIME 40.3 min
Reference: Aalizadeh et al. 2019
Chemical Composition of Buffer Solution. Iterative
Example:
AC$CHROMATOGRAPHY: SOLVENT A acetonitrile-methanol-water (19:19:2) with 0.1% acetic acid
AC$CHROMATOGRAPHY: SOLVENT B 2-propanol with 0.1% acetic acid and 0.1% ammonium hydroxide (28%)
Temperature of the Transferline between GC and MS instrument.
Example:
AC$CHROMATOGRAPHY: TRANSFERLINE_TEMPERATURE 200 C
Experimental Methods and Conditions which are not included in other sections. Optional
AC$GENERAL fields should be arranged by the alphabetical order of subtag names.
Concentration of Analytical Standard Used for the Generation of MassBank Records. The mandatory concentration unit is ug/L.
Example:
AC$GENERAL: CONCENTRATION 1 ug/L
ANALYTICAL_TIME
COLUMN_PRESSURE
INTERNAL_STANDARD
INTERNAL_STANDARD_MT
MIGRATION_TIME
PRECONDITIONING
RUNNING_BUFFER
RUNNING_VOLTAGE
SAMPLE_INJECTION
SAMPLING_CONE
SHEATH_LIQUID
TIME_PROGRAM
WASHING_BUFFER
Experimental Methods and Conditions of Ion Mobility Separation. Optional
AC$ION_MOBILITY fields should be arranged by the alphabetical order of subtag names.
Collisional Cross Section (CCS) obtained after calibration.
Example 1:
AC$CHROMATOGRAPHY: CCS 152.4
Drift gas used for ion mobility separation.
Example 1:
AC$CHROMATOGRAPHY: DRIFT_GAS Helium
Drift time in ms.
Example 1:
AC$CHROMATOGRAPHY: DRIFT_TIME 56.2
Type of ion mobility separation used.
Data of type AC$CHROMATOGRAPHY: INSTRUMENT_TYPE are:
DT
TWIMS
TIMS
Example 1:
AC$CHROMATOGRAPHY: INSTRUMENT_TYPE DT
Carrier Gas Used for GC-MS.
Example 1:
AC$CHROMATOGRAPHY: INVERSE_REDUCED_ION_MOBILITY 56.2
Information of Precursor or Molecular Ion. Optional
m/z of Base Peak.
Example:
MS$FOCUSED_ION: BASE_PEAK 73
Cross-reference to HUPO-PSI: precursor m/z [MS:1000504]
Molecular Formula of Derivative for GC-MS.
Example 1:
MS$FOCUSED_ION: DERIVATIVE_FORM C19H42O5Si4
Example 2:
MS$FOCUSED_ION: DERIVATIVE_FORM C{9+3*n}H{16+8*n}NO5Si{n}
Exact Mass of Derivative for GC-MS.
Example:
MS$FOCUSED_ION: DERIVATIVE_MASS 462.21093
Type of Derivative for GC-MS.
Example:
MS$FOCUSED_ION: DERIVATIVE_TYPE 4 TMS
Type of Focused Ion.
Example:
MS$FOCUSED_ION: ION_TYPE [M+H]+
Types currently used in MassBank are:
[M]+
[M]+*
[M+H]+
[2M+H]+
[M+Na]+
[M-H+Na]+
[2M+Na]+
[M+2Na-H]+
[(M+NH3)+H]+
[M+H-H2O]+
[M+H-C6H10O4]+
[M+H-C6H10O5]+
[M]-
[M-H]-
[M-2H]-
[M-2H+H2O]-
[M-H+OH]-
[2M-H]-
[M+HCOO]-
[(M+CH3COOH)-H]-
[2M-H-CO2]-
[2M-H-C6H10O5]-
Intensity of Focused Ion.
Example:
MS$FOCUSED_ION: PRECURSOR_INTENSITY 10000
m/z of Precursor Ion in MSn spectrum.
Example:
MS$FOCUSED_ION: PRECURSOR_M/Z 289.07123
Calculated exact mass is preferred to the measured accurate mass of the precursor ion.
Type of Precursor Ion in MSn spectrum.
Example for MS2:
MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
Example for MS3:
MS$FOCUSED_ION: PRECURSOR_TYPE [M+CH3COO]-/[M-CH3]-
The syntax is [<n>M<+-><molecular formula>]<charge>
Example:
[M]+
[M+Na]+
[2M-H]-
[2M-H-CO2]-
See see 2.5.1 mS$DATA_ION_TYPE for a full list.
Cross-reference to HUPO-PSI: isolation window attribute [MS: 1000792]
FULL_SCAN_FRAGMENT_ION_PEAK
Data Processing Method of Peak Detection. Optional
MS$DATA_PROCESSING fields should be arranged by the alphabetical order of subtag names. Cross-reference to HUPO-PSI: Data processing [MS:1000543]
Addtional Comments on Data Processing.
Example:
MS$DATA_PROCESSING: COMMENT Relative m/z normalised by peak(m/z=68.9396). set 999 for peak(m/z=568.9187,rel=1046).
Method for the Centroiding of Profile Data.
Example:
MS$DATA_PROCESSING: DEPROFILE Proteowizard 3.0.19022
Peak Detection.
Example:
MS$DATA_PROCESSING: FIND_PEAK Convexity search; threshold = 9.1
Data processing to include reanalyzed peaks (e.g. in RMassBank).
Example:
MS$DATA_PROCESSING: REANALYZE Peaks with additional N2/O included
Data processing to recalibrate mass accuracy (e.g. in RMassBank).
Example:
MS$DATA_PROCESSING: RECALIBRATE loess on assigned fragments and MS1
Whole Process in Single Method / Software.
Example:
MS$DATA_PROCESSING: WHOLE Analyst 1.4.2
Hashed Identifier of Mass Spectra. Mandatory and Single Line Information
Example:
PK$SPLASH: splash10-z200000000-87bb3c76b8e5f33dd07f
Chemical Annotation of Peaks with Molecular Formula. Optional and Multiple Line Information
Line 1 defines the record format of the annotation blocks. Contributors freely define the record format by using appropriate terms.
Line 2 or later：sequence of multiple line annotation blocks.
The first line of each annotation block should be indented by space space. The second or later line in each annotation block should be indented by space space space space.
Example 1:
PK$ANNOTATION: m/z annotation exact_mass error(ppm) formula
794.76 [PC(18:0,20:4)-CH3]- 794.56998 239 C45H81NO8P
Example 2:
PK$ANNOTATION: m/z {annotation formula exact_mass error(ppm)}
494.34 [lyso PC(alkyl-18:0,-)]- C25H53NO6P 494.36105 -42
Example 3:
PK$ANNOTATION: m/z formula annotation exact_mass error(ppm)
167.08947 C9H12O2N [M+1]+(13C) 167.08961 0.81
168.08681 C9H12O2N [M+1]+(13C, 15N) 168.08664 1.04
Example 4: RMassBank provides the option for automated tentative annotation of the fragment peaks including in-source adduct fragments (N2/O)
PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm)
94.0656 C6H8N+ 1 94.0651 4.89
105.0702 C8H9+ 1 105.0699 3.36
106.0652 C7H8N+ 1 106.0651 0.52
107.0733 C7H9N+ 1 107.073 2.92
122.0968 C8H12N+ 1 122.0964 3
133.0766 C8H9N2+ 1 133.076 4.34
The automated annotation by RMassBank is currently tentative.
See Section 2.7.2 about more details of Example 3.
Total Number of Peaks in PK$PEAK (2.6.4). Mandatory
Example:
PK$NUM_PEAK: 86
Peak Data. Mandatory and Multiple line Information
Example:
PK$PEAK: m/z int. rel.int.
326.65 5.3 5
328.28 7.6 7
Line 1: fixed string which denotes the format of Line 2 or later.
PK$PEAK: m/z int. rel.int.
Line 2 or later: space space M/Z space INT space REL
- M/Z: m/z of the peak.
- INT: intensity of the peak.
- REL: an integer from 1 to 999 which denotes relative intensity of the peak.
Peaks are arranged in the ascending order of m/z.
This section will be updated in near future as molfiles are deprecated
This section defines the chemical information of isotope-labeled chemical compounds. CH$NAME is Chemical Name followed by ”–[(Labeled Positions-)Isotopic Atom Name with the Number of Isotopic Atoms]”.
Examples:
CH$NAME: Glycine-[2-13C, 15N]
CH$NAME: L-Aspartic acid-[2-15N][3,3-d2]
CH$NAME: Benzene-[d6]
MOLFILE depends on whether the labeled position is specified. If the labeled position is specified, molfile defines the isotopic atom name and the labeled position. Otherwise molfile should be the same to that of the non-labeled chemical compound. CH$FORMULA should be the same to that of the non-labeled chemical compound. CH$EXACT_MASS is the monoisotopic mass, but not the sum of the mass of the isotopes. Thus CH$EXACT_MASS should be equal to that of the non-labeled chemical compound. CH$SMILES is the same to that of the non-labeled chemical compound. CH$IUPAC, which is InChI code, should define the isotope name and the labeled positions if these two are specified. If not, InChI code is the same to that of the non-labeled chemical compound. MS$FOCUSED_ION: PRECURSOR_M/Z should be the value that was actually used in the mass spectrometry. MS$FOCUSED_ION: PRECURSOR_TYPE should be the same to that of non-labeled chemical compound.
Example:
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
Record Editor correctly generates CH$FORMULA, CH$EXACT_MASS, CH$SMILES, and CH$IUPAC from the molfile of the isotope-labeled chemical compound.
This section describes the annotation of natural abundant isotopic peaks. Optional and Multiple Line Information.
Example:
PK$ANNOTATION: m/z formula annotation exact_mass error(ppm)
167.08947 C9H12O2N [M+1]+(13C) 167.08961 0.81
168.08681 C9H12O2N [M+1]+(13C, 15N) 168.08664 1.04
Line 1 defines the record format of Line 2 or later lines. The first line of each annotation block should be indented by space space.