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10 changes: 10 additions & 0 deletions Rscript/Library/mzkit_app/@export/massbank.d.ts
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Expand Up @@ -39,6 +39,16 @@ declare namespace massbank {
* @param chebi the chebi ontology data, in clr type: @``T:SMRUCC.genomics.foundation.OBO_Foundry.IO.Models.OBOFile``
*/
function extract_chebi_compounds(chebi: object): object;
/**
* Extract the unique metabolite information from the mona database
*
*
* @param mona -
* @param env -
*
* + default value Is ``null``.
*/
function extract_mona_metabolites(mona: any, env?: object): any;
module glycosyl {
/**
* @param rules default value Is ``null``.
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1 change: 1 addition & 0 deletions Rscript/Library/mzkit_app/man/mzkit/massbank/massbank.md
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Expand Up @@ -8,6 +8,7 @@ Metabolite annotation database toolkit
+ [read.RefMet](massbank/read.RefMet.1) read the csv table of refmet
+ [read.lotus](massbank/read.lotus.1) load the lotus natural products metabolite library from a given file
+ [read.MoNA](massbank/read.MoNA.1) read MoNA database file.
+ [extract_mona_metabolites](massbank/extract_mona_metabolites.1) Extract the unique metabolite information from the mona database
+ [read.SDF](massbank/read.SDF.1) read metabolite data in a given sdf data file.
+ [write.lipidmaps](massbank/write.lipidmaps.1) save lipidmaps data repository.
+ [read.lipidmaps](massbank/read.lipidmaps.1) read lipidmaps messagepack repository file
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.\" man page create by R# package system.
.TH MASSBANK 1 2000-Jan "extract_mona_metabolites" "extract_mona_metabolites"
.SH NAME
extract_mona_metabolites \- Extract the unique metabolite information from the mona database
.SH SYNOPSIS
\fIextract_mona_metabolites(\fBmona\fR as any,
[\fB<Environment>\fR]);\fR
.SH DESCRIPTION
.PP
Extract the unique metabolite information from the mona database
.PP
.SH OPTIONS
.PP
\fBmona\fB \fR\- -.
.PP
.PP
\fBenv\fB \fR\- -.
.PP
.SH SEE ALSO
massbank
.SH FILES
.PP
mzkit.dll
.PP
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<!DOCTYPE html>
<html>

<head>
<title>BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations.ICompoundNameProvider</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
<link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
</head>

<body>
<div class="container">

<table style="width: 100%;">
<tr>
<td>ICompoundNameProvider {BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations}</td>
<td style="text-align: right;">.NET clr documentation</td>
</tr>
</table>

<h2>ICompoundNameProvider</h2>

<h3>Description</h3>

<p>An interface for provides the metabolite common names</p>

<h3>Declare</h3>

<pre>
<code id="clr_ts">
# namespace BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations
export class ICompoundNameProvider {
CommonName: string;
}
</code>
</pre>

<h3>.NET clr type reference tree</h3>

this clr type has no other .net clr type reference.


<hr />
<div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
href="../{$package}.html">Index</a>]
</div>
</div>
</body>

<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
<script type="text/javascript">r_highlights("clr_ts");</script>

</html>
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<!DOCTYPE html>
<html>

<head>
<title>BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations.IExactMassProvider</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
<link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
</head>

<body>
<div class="container">

<table style="width: 100%;">
<tr>
<td>IExactMassProvider {BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations}</td>
<td style="text-align: right;">.NET clr documentation</td>
</tr>
</table>

<h2>IExactMassProvider</h2>

<h3>Description</h3>

<p>An interface for provides the exact mass value</p>

<p>The mass recorded by a mass spectrometer can refer to different physical
quantities depending on the characteristics of the instrument and the
manner in which the mass spectrum is displayed.

## Units

The dalton(symbol: Da) Is the standard unit that Is used for indicating
mass on an atomic Or molecular scale (atomic mass).[1] The unified atomic
mass unit (symbol: u) Is equivalent to the dalton. One dalton Is
approximately the mass of one a single proton Or neutron.[2] The unified
atomic mass unit has a value of 1.660538921(73)×10−27 kg.[3] The amu
without the "unified" prefix Is an obsolete unit based on oxygen, which
was replaced in 1961.

## Molecular mass</p>

<p>Theoretical isotope distribution For the molecular ion Of caffeine
The molecular mass (abbreviated Mr) Of a substance, formerly also called
molecular weight And abbreviated As MW, Is the mass Of one molecule Of
that substance, relative To the unified atomic mass unit u (equal To 1/12
the mass Of one atom Of 12C). Due To this relativity, the molecular mass
Of a substance Is commonly referred To As the relative molecular mass,
And abbreviated To Mr.

## Average mass

The average mass Of a molecule Is obtained by summing the average atomic
masses Of the constituent elements. For example, the average mass Of
natural water With formula H2O Is

1.00794 + 1.00794 + 15.9994 = 18.01528 Da.

## Mass number

The mass number, also called the nucleon number, Is the number Of protons
And neutrons In an atomic nucleus. The mass number Is unique For Each
isotope Of an element And Is written either after the element name Or As
a superscript To the left Of an element's symbol. For example, carbon-12
(12C) has 6 protons and 6 neutrons.

## Nominal mass

The nominal mass For an element Is the mass number Of its most abundant
naturally occurring stable isotope, And For an ion Or molecule, the nominal
mass Is the sum Of the nominal masses Of the constituent atoms.[4][5]
Isotope abundances are tabulated by IUPAC:[6] for example carbon has two
stable isotopes 12C at 98.9% natural abundance And 13C at 1.1% natural
abundance, thus the nominal mass of carbon Is 12. The nominal mass Is Not
always the lowest mass number, for example iron has isotopes 54Fe, 56Fe,
57Fe, And 58Fe with abundances 6%, 92%, 2%, And 0.3%, respectively, And a
nominal mass of 56 Da. For a molecule, the nominal mass Is obtained by
summing the nominal masses of the constituent elements, for example water
has two hydrogen atoms with nominal mass 1 Da And one oxygen atom with nominal
mass 16 Da, therefore the nominal mass of H2O Is 18 Da.

In mass spectrometry, the difference between the nominal mass And the
monoisotopic mass Is the mass defect.[7] This differs from the definition
of mass defect used in physics which Is the difference between the mass of
a composite particle And the sum of the masses of its constituent parts.[8]

## Accurate mass

The accurate mass (more appropriately, the measured accurate mass[9]) Is an
experimentally determined mass that allows the elemental composition To be
determined.[10] For molecules With mass below 200 Da, 5 ppm accuracy Is often
sufficient To uniquely determine the elemental composition.[11]

## Exact mass

The exact mass Of an isotopic species (more appropriately, the calculated
exact mass[9]) Is obtained by summing the masses Of the individual isotopes
Of the molecule. For example, the exact mass Of water containing two hydrogen-1
(1H) And one oxygen-16 (16O) Is 1.0078 + 1.0078 + 15.9949 = 18.0105 Da.
The exact mass Of heavy water, containing two hydrogen-2 (deuterium Or 2H)
And one oxygen-16 (16O) Is 2.0141 + 2.0141 + 15.9949 = 20.0229 Da.</p>

<p>When an exact mass value Is given without specifying an isotopic species, it
normally refers to the most abundant isotopic species.

## Monoisotopic mass
Main article: monoisotopic mass
The monoisotopic mass Is the sum Of the masses Of the atoms In a molecule Using
the unbound, ground-state, rest mass Of the principal (most abundant) isotope
For Each element.[12][5] The monoisotopic mass Of a molecule Or ion Is the exact
mass obtained Using the principal isotopes. Monoisotopic mass Is typically
expressed In daltons.</p>

<p>For typical organic compounds, where the monoisotopic mass Is most commonly used,
this also results in the lightest isotope being selected. For some heavier atoms
such as iron And argon the principal isotope Is Not the lightest isotope. The
mass spectrum peak corresponding To the monoisotopic mass Is often Not observed
For large molecules, but can be determined from the isotopic distribution.

## Most abundant mass</p>

<p>Theoretical isotope distribution For the molecular ion Of glucagon (C153H224N42O50S)

This refers To the mass Of the molecule With the most highly represented isotope
distribution, based On the natural abundance Of the isotopes.

## Isotopomer and isotopologue

Isotopomers (isotopic isomers) are isomers having the same number of each isotopic
atom, but differing in the positions of the isotopic atoms.[15] For example,
CH3CHDCH3 And CH3CH2CH2D are a pair of structural isotopomers.</p>

<p>Isotopomers should Not be confused With isotopologues, which are chemical species
that differ In the isotopic composition Of their molecules Or ions. For example,
three isotopologues Of the water molecule With different isotopic composition Of
hydrogen are: HOH, HOD And DOD, where D stands for deuterium (2H).

## Kendrick mass

The Kendrick mass Is a mass obtained by multiplying the measured mass by a numeric
factor. The Kendrick mass Is used To aid In the identification Of molecules Of similar
chemical Structure from peaks In mass spectra.[16][17] The method Of stating mass was
suggested In 1963 by the chemist Edward Kendrick.</p>

<p>According to the procedure outlined by Kendrick, the mass of CH2 Is defined as 14.000 Da,
instead of 14.01565 Da.[18][19]</p>

<p>The Kendrick mass For a family Of compounds F Is given by[20]</p>

<p>Kendrick mass = (observed mass)×nominal mass()exact mass</p>

<p>{\displaystyle {\mbox{Kendrick mass}}~(F)=({\mbox{observed mass}})\times {\frac {{\mbox{nominal mass}}~(F)}{{\mbox{exact mass}}~(F)}}.}

For hydrocarbon analysis, F = CH2.

## Mass defect (mass spectrometry)

The mass defect used In nuclear physics Is different from its use In mass spectrometry.
In nuclear physics, the mass defect Is the difference In the mass Of a composite particle
And the sum Of the masses Of its component parts. In mass spectrometry the mass defect
Is defined As the difference between the exact mass And the nearest Integer mass.[21][22]</p>

<p>The Kendrick mass defect Is the exact Kendrick mass subtracted from the nearest Integer
Kendrick mass.[23]</p>

<p>Mass defect filtering can be used To selectively detect compounds With a mass spectrometer
based On their chemical composition.[7]

## Packing fraction (mass spectrometry)</p>

<p>Francis William Aston won the 1922 Nobel Prize In Chemistry For his discovery, by means
Of his mass spectrograph, Of isotopes, In a large number Of non-radioactive elements,
And For his enunciation Of the whole number rule.[24][25]

The term packing fraction was defined by Aston As the difference Of the measured mass M And
the nearest Integer mass I (based On the oxygen-16 mass scale) divided by the quantity
comprising the mass number multiplied by ten thousand:[26]</p>

<p>{\displaystyle f={\frac {M-I}{10^{4}\ I}}}.</p>

<p>Aston's early model of nuclear structure (prior to the discovery of the neutron) postulated
that the electromagnetic fields of closely packed protons and electrons in the nucleus would
interfere and a fraction of the mass would be destroyed.[27] A low packing fraction is
indicative of a stable nucleus.[28]

## Nitrogen rule

The nitrogen rule states that organic compounds containing exclusively hydrogen, carbon,
nitrogen, oxygen, silicon, phosphorus, sulfur, And the halogens either have an odd nominal
mass that indicates an odd number Of nitrogen atoms are present Or an even nominal mass that
indicates an even number Of nitrogen atoms are present In the molecular ion.[29][30]

## Prout's hypothesis and the whole number rule

The whole number rule states that the masses Of the isotopes are Integer multiples Of the mass
Of the hydrogen atom.[31] The rule Is a modified version Of Prout's hypothesis proposed in 1815,
to the effect that atomic weights are multiples of the weight of the hydrogen atom.[32]</p>

<h3>Declare</h3>

<pre>
<code id="clr_ts">
# namespace BioNovoGene.Analytical.MassSpectrometry.Math.Ms1.Annotations
export class IExactMassProvider {
# The exact mass of an isotopic species (more appropriately, the calculated exact mass)
# is obtained by summing the masses of the individual isotopes of the molecule. For
# example, the exact mass of water containing two hydrogen-1 (1H) and one oxygen-16 (16O)
# is 1.0078 + 1.0078 + 15.9949 = 18.0105 Da. The exact mass of heavy water, containing
# two hydrogen-2 (deuterium or 2H) and one oxygen-16 (16O) is
# 2.0141 + 2.0141 + 15.9949 = 20.0229 Da.
#
# When an exact mass value Is given without specifying an isotopic species, it normally
# refers to the most abundant isotopic species.
ExactMass: double;
}
</code>
</pre>

<h3>.NET clr type reference tree</h3>

this clr type has no other .net clr type reference.


<hr />
<div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
href="../{$package}.html">Index</a>]
</div>
</div>
</body>

<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
<script type="text/javascript">r_highlights("clr_ts");</script>

</html>
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