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<!DOCTYPE html>
<html lang="en">
<head>
<title>MZKit | Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS
raw data, chemoinformatics data analysis and data visualization.</title>
<!-- Meta -->
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">
<link rel="shortcut icon" href="favicon.ico">
<link rel="manifest" href="./manifest.json">
<link href='https://fonts.googleapis.com/css?family=Lato:300,400,300italic,400italic' rel='stylesheet'
type='text/css'>
<link href='https://fonts.googleapis.com/css?family=Montserrat:400,700' rel='stylesheet' type='text/css'>
<!-- FontAwesome JS-->
<script defer src="assets/fontawesome/js/all.min.js"></script>
<!-- Global CSS -->
<link rel="stylesheet" href="assets/plugins/bootstrap/css/bootstrap.min.css">
<!-- Plugins CSS -->
<link rel="stylesheet" href="assets/plugins/prism/prism.css">
<!-- Theme CSS -->
<link id="theme-style" rel="stylesheet" href="assets/css/theme-1.css">
<link id="theme-style" rel="stylesheet" href="assets/css/slider.css">
<!-- GitHub Button -->
<script async defer src="https://buttons.github.io/buttons.js"></script>
<style>
.hero-section .figure-holder {
background: url(./assets/images/2a5276fe-e357-4312-a75b-7064577b5261.png) no-repeat right top;
background-size: 1000px auto;
min-height: 640px;
}
.hero-section {
padding-top: 50px;
text-shadow: 2px 2px 18px #738fc5;
}
.pt-md-4 {
padding-top: 1.5rem !important;
}
.pt-3 {
padding-top: 1rem !important;
}
.site-tagline {
color: white;
}
.app-badge-img {
height: 64px;
}
</style>
</head>
<body data-spy="scroll">
<!-- ******HEADER****** -->
<header id="header" class="header">
<nav id="main-nav" class="main-nav navbar navbar-expand-md">
<div class="container-fluid">
<a class="navbar-brand logo scrollto" href="#promo">
<span class="logo-title">MZKit</span>
</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-collapse"
aria-controls="navbar-collapse" aria-expanded="false" aria-label="Toggle navigation">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<!--//nav-toggle-->
<div class="navbar-collapse collapse" id="navbar-collapse">
<ul id="nav-menu" class="nav navbar-nav ms-md-auto">
<li class="nav-item sr-only"><a class="nav-link scrollto" href="#promo">Home</a></li>
<li class="nav-item"><a class="nav-link scrollto" href="#about">About</a></li>
<li class="nav-item"><a class="nav-link scrollto" href="#features">Features</a></li>
<li class="nav-item"><a class="nav-link" href="./HISTORY.html">History</a></li>
<li class="nav-item"><a class="nav-link" href="./zh/">Docs</a></li>
<li class="nav-item"><a class="nav-link scrollto" href="#license">License</a></li>
<li class="nav-item last"><a class="nav-link scrollto" href="#contact">Contact</a></li>
</ul>
<!--//nav-->
</div>
<!--//navabr-collapse-->
</div>
</nav>
<!--//main-nav-->
</header>
<!--//header-->
<!-- ******PROMO****** -->
<section id="promo" class="promo section offset-header">
<br />
<br />
<br />
<div class="container text-center banner">
<h1 class="title" style="color: white;text-shadow: 2px 2px 32px #ffffff9c;">MZ<span
class="highlight">Kit</span>
</h1>
<p class="intro">Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS
and GC-MS raw data, chemoinformatics data analysis and data visualization.</p>
<div class="btns">
<a class="btn btn-cta-secondary" href="./zh/" target="_blank">Documentation</a>
<!-- <a class="btn btn-cta-primary" href="http://www.biodeep.cn/downloads?lang=en-US"
target="_blank">Download</a> -->
<a class="btn btn-cta-primary" href="/download.html" target="_blank"><i
class="fas fa-cloud-download"></i>Download</a>
</div>
<br />
<!--
<ul class="meta list-inline">
<li class="list-inline-item"><a href="https://github.com/xieguigang/mzkit" target="_blank">View on
GitHub</a></li>
<li class="list-inline-item"><a
href="/docs"
target="_blank">Full Documentation</a></li>
<li class="list-inline-item">Created by: <a
href="https://github.com/xieguigang/"
target="_blank">xieguigang</a></li>
</ul>
-->
</div>
<br />
<br />
<br />
<br />
<br />
<br />
<!--//container-->
<div class="social-media">
<div class="social-media-inner container text-center">
<ul class="list-inline mb-2">
<!--// Generate github buttons: https://github.com/mdo/github-buttons -->
<li class="list-inline-item github-star">
<a class="github-button" href="https://github.com/xieguigang/mzkit" data-icon="octicon-star"
aria-label="Star xieguigang/mzkit on GitHub">Star</a>
</li>
<li class="list-inline-item github-follow">
<!-- Place this tag where you want the button to render. -->
<a class="github-button" href="https://github.com/xieguigang/"
aria-label="Follow @xieguigang on GitHub">Follow @xieguigang</a>
</li>
</ul>
</div>
</div>
</section>
<!--//promo-->
<!-- ******ABOUT****** -->
<section id="about" class="about section">
<div class="container">
<h2 class="title text-center">What is MZKit? <a href="https://doi.org/10.5281/zenodo.4603277"><img
src="https://zenodo.org/badge/DOI/10.5281/zenodo.4603277.svg" alt="DOI"></a></h2>
<p class="intro text-center">Mzkit is an open source raw data file toolkit for mass spectrometry data
analysis, provides by the BioNovoGene corporation. The features of mzkit inlcudes: raw data file content
viewer(XIC/TIC/Mass spectrum plot/MS-Imaging), build molecule network, formula de-novo search, de-novo
annotation of the unknown metabolite features, MALDI single cell metabolomics data analysis,
pathological slide viewer and targeted data quantification.</p>
<div class="row">
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-heart"></i>
</div>
<div class="content">
<h3 class="sub-title">Designed for developers</h3>
<p>The MZKit project its source code is open sourced on <a
href="https://github.com/xieguigang/mzkit">github</a> and totally free of charge for
used in
your academic project.</p>
</div>
<!--//content-->
</div>
<!--//item-->
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-clock"></i>
</div>
<div class="content">
<h3 class="sub-title">Time saver</h3>
<p>MZKit is easily to learn and also work in fast speed. You also can running the MZKit R#
script in parallel for deal with the large scale metabolomics raw data files.</p>
</div>
<!--//content-->
</div>
<!--//item-->
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-crosshairs"></i>
</div>
<div class="content">
<h3 class="sub-title">Focused Metabolomics</h3>
<p>
The development of the MZKit workbench software is mainly address of the metabolomics raw
data processing and raw data visualization.
</p>
</div>
<!--//content-->
</div>
<!--//item-->
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-mobile-alt"></i>
</div>
<div class="content">
<h3 class="sub-title">User-friendly</h3>
<p>The MZKit workbench has a user friendly UI, which means you don't needs to do some scripting
programming for run data analysis of your mass spectrum raw data file.</p>
</div>
<!--//content-->
</div>
<!--//item-->
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-code"></i>
</div>
<div class="content">
<h3 class="sub-title">Easy to automation</h3>
<p>You can create a mass spectrum data analysis pipeline on a windows server via scripting in R#
programming language. The MZKit software is written in VisualBasic.NET language, and you
also can build a software by using the MZKit library in your .NET program.</p>
</div>
<!--//content-->
</div>
<!--//item-->
<div class="item col-lg-4 col-md-6 col-12">
<div class="icon-holder">
<i class="fa-solid fa-coffee"></i>
</div>
<div class="content">
<h3 class="sub-title">Tutorials video</h3>
<p>Watch the MZKit tutorial video on <a
href="https://www.bilibili.com/video/BV1rX4y157XP?spm_id_from=333.999.0.0&vd_source=19862965907c94b467a9fd0c99ed2f31">BILIBILI</a>
which we created for the audience like you.
</p>
<p>
<i class="fa-solid fa-arrow-right"></i> <a href="./bilibili.html#tutorials">MZKit
Video
Tutorials</a> from <span style="text-shadow: 2px 2px 18px #193977;">“六神无主鸠”</span>
</p>
</div>
<!--//content-->
</div>
<!--//item-->
</div>
<!--//row-->
</div>
<!--//container-->
</section>
<!--//about-->
<section class="hero-section">
<div class="container">
<div class="row figure-holder">
<div class="col-12 col-md-6 pt-3 pt-md-4" style="
background-color: #00000096;
padding-left: 40px;
">
<h2 class="site-headline font-weight-bold mt-lg-5 pt-lg-5">A ready-to-use toolbox for processing
your
metabolomics dataset and the biological knowledges.</h2>
<div class="site-tagline mb-3">Simply and easily enough for handling the metabolomics rawdata,
interpret your data，visualize your data and take a deep look inside into the biological
knowledges!</div>
<div class="cta-btns">
<div class="mb-4"><a class="btn btn-primary font-weight-bold theme-btn" href="">View
Documents</a></div>
<ul class="app-stores list-unstyled list-inline mx-auto mx-md-0 d-inline-block">
<li class="list-inline-item me-3"><a href="./download.html"><img class="app-badge-img"
src="./assets/images/windows-app-badge.png" alt="Windows App"></a></li>
<li class="list-inline-item"><a href="./docker.html"><img class="app-badge-img"
src="./assets/images/docker-app-badge.png" alt="Linux Docker"></a></li>
</ul>
</div>
</div>
</div>
<!--//row-->
</div>
</section>
<!--//hero-section-->
<div id="features" class="section">
<div class="container text-center">
<h2 class="section-title" style="margin: 0;
margin-bottom: 15px;
font-size: 36px;
font-weight: 300; color: var(--bs-heading-color);
text-shadow: 2px 2px 18px #193977;">Discover Features
</h2>
<p class="intro" style="color: #8e949e;
font-size: 16px;
max-width: 760px;
margin: 0 auto;
margin-bottom: 60px;">
There ares some awesome features of MZKit workbench that wait for discovered by you. Download and
install MZKit and then try to find out them!<br />
<br />
<a href="https://bio.tools/mzkit">
<img src="assets/images/opeb_logo.gif" style="height: 72px;">
</a>
<a href="https://scicrunch.org/resolver/RRID:SCR_023936?q=&i=rrid:scr_023936">
<img src="assets/images/rin-resources_136123.png" style="height: 36px;">
</a>
</p>
<div class="tabbed-area row">
<!-- Nav tabs -->
<div class="feature-nav nav nav-pill flex-column col-lg-4 col-md-6 col-12 order-0 order-md-1"
role="tablist" aria-orientation="vertical" style="margin-top: 30px;
padding-left: 15px; text-align: left">
<div><strong>Click this feature list to discover</strong></div>
<hr />
<a class="nav-link mb-lg-3" href="#feature-1" aria-controls="feature-1" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-magic me-2"></i>
View TIC/BPC/XIC chromatography plot
</a>
<a class="nav-link mb-lg-3" href="#feature-2" aria-controls="feature-2" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-cubes me-2"></i>
KEGG biological function data analysis
</a>
<a class="nav-link mb-lg-3 active" href="#feature-3" aria-controls="feature-3" data-bs-toggle="pill"
role="tab" aria-selected="true">
<i class="fa-solid fa-chart-bar me-2"></i>
MS-Imaging Viewer
</a>
<a class="nav-link mb-lg-3" href="#feature-4" aria-controls="feature-4" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-code me-2"></i>
Mass spectrum alignment
</a>
<a class="nav-link mb-lg-3" href="#feature-5" aria-controls="feature-5" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-rocket me-2"></i>
Mass spectrum molecule networking
</a>
<a class="nav-link mb-lg-3" href="#feature-6" aria-controls="feature-6" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-mobile-alt me-2"></i>
LC-MS raw data viewer and data inspector
</a>
<a class="nav-link mb-lg-3" href="#feature-7" aria-controls="feature-7" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-star me-2"></i>
Targetted metabolomics linear modelling
</a>
<a class="nav-link mb-lg-3" href="#feature-8" aria-controls="feature-8" data-bs-toggle="pill"
role="tab" aria-selected="false" tabindex="-1">
<i class="fa-solid fa-heart me-2"></i>
R# automation your analysis work
</a>
</div>
<!-- Tab panes -->
<div class="feature-content tab-content col-lg-8 col-md-6 col-12 order-1 order-md-0">
<div role="tabpanel" class="tab-pane fade" id="feature-1">
<a href="assets/images/screens/BPC_overlay.PNG" target="_blank" data-toggle="lightbox"
data-caption="Show BPC overlays between multiple sample raw data files to view the data variants."><img
class="img-fluid" src="assets/images/screens/BPC_overlay.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-2">
<a href="assets/images/screens/de-novo-formulas.png" target="_blank" data-toggle="lightbox"
data-caption="Run metadna annotation and KEGG pathway enrichment analysis of your metabolomics raw data file, powered by GCModeller."><img
class="img-fluid" src="assets/images/screens/de-novo-formulas.png" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade active show" id="feature-3">
<a href="assets/images/screens/ms-imaging2.PNG" target="_blank" data-toggle="lightbox"
data-caption="MS-Imaging view for visual of the spatial metabolomics raw data."><img
class="img-fluid" src="assets/images/screens/ms-imaging2.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-4">
<a href="assets/images/screens/MS.PNG" target="_blank" data-toggle="lightbox"
data-caption="Input a custom mass spectrum in ms level 2 and then search similar spectrum in all of your raw data files!"><img
class="img-fluid" src="assets/images/screens/MS.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-5">
<a href="assets/images/screens/network_viewer.PNG" target="_blank" data-toggle="lightbox"
data-caption="Molecule networking in MZKit workbench to discovery new natural product or drugs just like GNPS it does."><img
class="img-fluid" src="assets/images/screens/network_viewer.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-6">
<a href="assets/images/screens/raw-scatter.PNG" target="_blank" data-toggle="lightbox"
data-caption="Inspect your metabolomics raw data file, view mass spectrum, peak finding on XIC matrix data, etc"><img
class="img-fluid" src="assets/images/screens/raw-scatter.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-7">
<a href="assets/images/screens/Targeted.PNG" target="_blank" data-toggle="lightbox"
data-caption="Do linear fitting and quantification of your targetted metabolomics raw data."><img
class="img-fluid" src="assets/images/screens/Targeted.PNG" alt="screenshot"></a>
</div>
<div role="tabpanel" class="tab-pane fade" id="feature-8">
<a href="assets/images/screens/automation.PNG" target="_blank" data-toggle="lightbox"
data-caption="MZKit provides the R# nuget package for create an automation pipeline work based on the GCModeller Rstudio platform."><img
class="img-fluid" src="assets/images/screens/automation.PNG" alt="screenshot"></a>
</div>
</div>
<!--//feature-content-->
</div>
<!--//tabbed-area-->
<br />
<br />
<hr />
<div class="tabbed-area row" style="text-align:left ; ">
<h2>Feature Highlights</h2>
<br />
<div class="row" style="text-align:left ; ">
<div class="col-lg-4" role="tablist" aria-orientation="vertical" style="margin-top: 30px;
padding-left: 15px; text-align: left">
<p>
MS-Imaging data visualization of your biological samples in MZKit workbench can use for
compares
of your
multiple targeted metabolite compounds on one graphics canvas. Such data visualization of
the
metabolite can visual and compares of the spatial enrichment results for the multiple
targeted
drugs or metabolism products for your experiment design. It is useful for presenting the
biomarker in a spatially way by MS-imaging.
</p>
<p>
<i class="fa-solid fa-arrow-right"></i> Visit <a href="./gallery.html">Data
Visualization
Gallery</a> to learn more.
</p>
</div>
<div class="feature-content tab-content col-lg-8"
style="text-align: left ; padding-left: 5%; padding-top: 0%;">
<a class="modal-fullscreen" href="assets/images/MS-Imaging-highlights.png" target="_blank"
data-toggle="lightbox" data-size="fullscreen"
data-caption="MS-Imaging of your biological sample in well organized matrix layout template, no more style tweaking.">
<img class="img-fluid" src="assets/images/MS-Imaging-highlights.png"
style="width: 80%; box-shadow: 0 6px 26px 0 black;" alt="MS-Imaging highlights"></a>
</div>
</div>
</div>
<div class="tabbed-area row" style="text-align:left ; ">
<div style="height: 45px;"></div>
<div class="row" style="text-align:left ; ">
<div class="feature-content tab-content col-lg-10"
style="text-align: left ; padding-left: 5%; padding-top: 0%;">
<a class="modal-fullscreen" href="assets/videos/slide-viewer.mp4" target="_blank"
data-toggle="lightbox" data-size="fullscreen"
data-caption="View pathological section slide via MZKit.">
<img class="img-fluid card-img-top" src="assets/images/screens/slide_viewer.PNG"
style="width: 100%;" alt="View pathological section slide via MZKit."></a>
<br />
<br />
<p>
MZKit workbench is compatible with the Hamamatsu slide scanner pathological section raw data
file.
You can open & view a pathological slide image in ndpi format or tif format in mzkit.
Make
pathological tissue region annotation and then mapping to the MS-imaging raw data.
</p>
</div>
</div>
</div>
<br />
<br />
<div class="tabbed-area row" style="text-align:left ; width:100%">
<div class="card" style="width: 40%;">
<br />
<a href="assets/images/targeted-linear.png" target="_blank" data-toggle="lightbox"
data-size="fullscreen"
data-caption="Linear regression and quantification analysis of the target biomarker in MZKit.">
<img class="img-fluid card-img-top" src="assets/images/targeted-linear.png" style="width: 100%;"
alt="Targetted Linear"></a>
<div class="card-body">
<p class="card-text">
Targeted metabolomics is the study and analysis of specific metabolites, and it take parts
in
disease research, animal model verification, biomarker
discovery, disease diagnosis, drug development, drug screening, drug evaluation, clinical
research and plant metabolism research:
<ol>
<li>Validation </li>
<li>Hypothesis driven</li>
<li>
Absolute quantification of spesific features
Validation of identified feature (Requires
commercially available chemicalstandart
for validation)
</li>
</ol>
</p>
</div>
</div>
<div style="width: 5%;"> </div>
<div class="card" style="width: 40%;">
<br />
<a href="assets/images/RawScatter_2D.png" target="_blank" data-toggle="lightbox"
data-size="fullscreen"
data-caption="Scatter 2D plot of the LC-MS un-targeted metabolomics sample data file.">
<img class="img-fluid card-img-top" src="assets/images/RawScatter_2D.png" style="width: 100%;"
alt="LC-MS scatter 2D plot"></a>
<div class="card-body">
<p class="card-text">
Untargeted metabolomics is a "discovery mode" process and it relies on differential
comparison
between groups of samples (for example cases versus controls): Non-targeted metabolomics can
analyze metabolites derived from the organisms comprehensively
and systematically. It is an unbiased metabolomics analysis that can discover new
biomarkers.
</p>
</div>
</div>
</div>
<div class="tabbed-area row" style="text-align:left ; ">
<div style="height: 30px;"></div>
<div class="row" style="text-align:left ; ">
<div class="feature-content tab-content col-lg-8"
style="text-align: left ; padding-left: 5%; padding-top: 0%;">
<a class="modal-fullscreen" href="assets/videos/scatter-viewer.mp4" target="_blank"
data-toggle="lightbox" data-size="fullscreen"
data-caption="LCMS data visualization in 3d viewer">
<img class="img-fluid card-img-top" src="assets/images/screens/LCMS-viewer.PNG"
style="width: 100%;" alt="LCMS data visualization"></a>
</div>
</div>
</div>
<div class="tabbed-area row" style="text-align:left ; ">
<div style="height: 30px;"></div>
<div class="row" style="text-align:left ; ">
<div class="feature-content tab-content col-lg-8"
style="text-align: left ; padding-left: 5%; padding-top: 0%;">
<a class="modal-fullscreen" href="assets/videos/smiles-cfm-id-workflow.mp4" target="_blank"
data-toggle="lightbox" data-size="fullscreen"
data-caption="Molecular structure drawing in MZKit">
<img class="img-fluid card-img-top" src="assets/images/screens/Chemoinformatics.PNG"
style="width: 100%;" alt="Chemoinformatics data processing"></a>
<br />
<br />
<p>
Draw chemical molecule structure via <a
href="https://lifescience.opensource.epam.com/ketcher/index.html"
target="__blank">Ketcher</a> in MZKit, and then convert the molecule structure data as
the SMILES/InChI string. Then we could do mass spectrum prediction in MZKit via calling
CFM-ID tool for generates the in-silicon MS2 matrix, finally search your MS2 matrix inside
multiple sample that which has been loaded into the MZKit workspace.
</p>
</div>
</div>
</div>
<br />
<hr />
<div style="text-align:left ;">
<h2>Runtime & System Requirements</h2>
<p>
MZKit workbench software required of .NET Framework 4.8 runtime:<br />
<a
href="https://dotnet.microsoft.com/download/dotnet-framework/net48">https://dotnet.microsoft.com/download/dotnet-framework/net48</a><br />
Rstudio application for run mzkit R# automation pipeline required of .NET Core 6.0(windows-x64)
runtime:<br />
<a
href="https://dotnet.microsoft.com/en-us/download/dotnet/6.0">https://dotnet.microsoft.com/en-us/download/dotnet/6.0</a><br />
The Microsoft WebView2 runtime(windows-x64) is required for some interactive data visualization and
analysis report generation:<br />
<a
href="https://developer.microsoft.com/en-us/microsoft-edge/webview2/#download-section">https://developer.microsoft.com/en-us/microsoft-edge/webview2/</a><br />
Unidata netCDF-C library is required for read GCxGC or GCMS netCDF rawdata file:<br />
<a
href="https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netCDF4.9.2-NC4-64.exe">https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netCDF4.9.2-NC4-64.exe</a>
</p>
<p>
MZKit workbench supports Windows 10/11 64Bit system and Windows Server 2016/2019/2022.
</p>
<p>
Hardware Requirement:
<ul>
<li>
CPU: 3.0GHz CPU with 2 Core at least, latest Intel i7/i9/E3 CPU or Intel Xeon Gold 6250 is
recommended.
</li>
<li>
Memory: 16GB DDR3 is required, 32GB DDR4 or higher is recommended.
</li>
<li>
Screen Resolution: 1600x900(minimal), 1920x1080 or above is recommended.
</li>
<li>
Graphics Card: NVIDIA GeForce GTX 1060 3GB or higher is recommended.
</li>
</ul>
</p>
</div>
</div>
<!--//container-->
</div>
<!--//features-->
<!-- ******LICENSE****** -->
<section id="license" class="license section">
<div class="container">
<div class="license-inner" style="box-shadow: 0 6px 26px 0 rgb(31 36 38 / 15%); max-width: 950px">
<h2 class="title text-center">License & Copyright</h2>
<p>
<strong>You can cite MZKit in your literature work if needed:</strong> xie, guigang &
BioNovoGene. BioNovoGene
mzkit: Data toolkits for processing NMR, MALDI MSI, LC-MS and GC-MS raw data, chemoinformatics data
analysis and data visualization. (2022) doi:<a
href="https://explore.openaire.eu/search/software?pid=10.5281%2Fzenodo.4603277">10.5281/zenodo.7040586</a>.
<br />
<ul>
<li>mzkit on ELIXIR biotools: <a href="https://bio.tools/mzkit">https://bio.tools/mzkit</a></li>
<li>mzkit on SciCrunch: <a
href="https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_023936/resolver?q=SCR_023936&l=SCR_023936&i=rrid:scr_023936">RRID:SCR_023936</a>
</li>
</ul>
<br />
<ul>
<li>
MZKit® is a registered trademark of BioNovoGene Corporation, protected by copyright law
and
international treaties.
</li>
<li>
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All
rights
reserved.
</li>
<li>
MS-DIAL was launched as a universal program for untargeted metabolomics that supports
multiple
instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker,
LECO, Sciex,
Shimadzu, Thermo, and Waters). Part of the spectrum algorithm in MZKit is developed
based on the
<a href="http://prime.psc.riken.jp/compms/msdial/main.html">MS-DIAL project</a>.
</li>
</ul>
</p>
<br />
<h3 class="title">MIT License</h3>
<div class="info" style="text-align:justify;">
<p style="text-align:justify;">
Copyright (c) 2018 [email protected], BioNovoGene Co., LTD.<br />
<br />
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:<br />
<br />
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.<br />
<br />
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
</p>
</div>
<br />
<h3 class="title">Reference</h3>
<p>
The development of the MZKit workbench library based on these works, you are also can cite
these
works if you use MZkit software:
</p>
<ol>
<li>
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding
Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted
Metabolomics, Nature Communications, 2019, 10: 1516.
</li>
<li>
Li S, Park Y, Duraisingham S, Strobel FH, Khan N, et al. (2013) Predicting Network
Activity from
High Throughput Metabolomics. PLOS Computational Biology 9(7): e1003123.
https://doi.org/10.1371/journal.pcbi.1003123
</li>
<li>
Pang, Z., Chong, J., Zhou, G., Morais D., Chang, L., Barrette, M., Gauthier, C.,
Jacques, PE.,
Li, S., and Xia, J. (2021) MetaboAnalyst 5.0: narrowing the gap between raw spectra and
functional insights Nucl. Acids Res. (doi: 10.1093/nar/gkab382)
</li>
<li>
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). KEGG:
Kyoto
Encyclopedia of Genes and Genomes. Nucleic acids research, 27(1), 29–34.
https://doi.org/10.1093/nar/27.1.29
</li>
<li>
Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M.,
VanderGheynst,
J., Fiehn, O., & Arita, M. (2015). MS-DIAL: data-independent MS/MS deconvolution for
comprehensive metabolome analysis. Nature methods, 12(6), 523–526.
https://doi.org/10.1038/nmeth.3393
</li>
<li>
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz
CR,
Russell DW, Subramaniam S., LMSD: LIPID MAPS® structure database Nucleic Acids Research,
35: p.
D527-32., DOI: 10.1093/nar/gkl838 , PMID: 17098933
</li>
<li>
Fahy E, Sud M, Cotter D & Subramaniam S., LIPID MAPS® online tools for lipid research
Nucleic
Acids Research (2007), 35: p. W606-12., DOI: 10.1093/nar/gkm324 , PMID: 17584797
</li>
<li>
Wishart DS, Guo AC, Oler E, et al., HMDB 5.0: the Human Metabolome Database for 2022.
Nucleic
Acids Res. 2022. Jan 7;50(D1):D622–31. 34986597
</li>
<li>
Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao
Peng, Don
Duy Nguyen et al. "Sharing and community curation of mass spectrometry data with Global
Natural
Products Social Molecular Networking." Nature biotechnology 34, no. 8 (2016): 828. PMID:
27504778
</li>
<li>Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product
similarity for
small-molecule compound identification. Nat Methods 18, 1524–1531 (2021).
https://doi.org/10.1038/s41592-021-01331-z
</li>
<li>Kind, T., Fiehn, O. Seven Golden Rules for heuristic filtering of molecular formulas
obtained by
accurate mass spectrometry. BMC Bioinformatics 8, 105 (2007).
https://doi.org/10.1186/1471-2105-8-105
</li>
</ol>
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<section id="contact" class="contact section has-pattern">
<div class="container">
<div class="contact-inner">
<h2 class="title text-center">Contact</h2>
<p class="intro text-center">I hope you find this MZKit software useful. <br />Feel free to get in
touch if you have any questions or suggestions.</p>
<div class="author-message">
<div class="profile">
<img class="img-fluid" src="assets/images/profile.png" alt="" />
</div>
<!--//profile-->
<div class="speech-bubble" style="box-shadow: 0 6px 20px 0 rgb(31 36 38 / 15%);">
<h3 class="sub-title">Wanna to get supports or make contribution to MZKit?</h3>
<p><a href="mailto://[email protected]" target="_blank">Get in touch with me </a> if you
encounter any problem when running the MZKit workbench software; And you also can prompt or
request a
new data analysis feature for make improvements of the MZKit workbench software.</p>
<div class="source">
<span class="name"><a href="https://stack.xieguigang.me/"
target="_blank">Xieguigang</a></span>
<br />
<span class="title">Senior Data Scientist <a href="https://panomix.com/">at
PANOMIX</a></span>
</div>
<!--//source-->
</div>
<!--//speech-bubble-->
</div>
<!--//author-message-->
<div class="info text-center">
<h4 class="sub-title">External Links</h4>
<ul class="list-inline">
<li class="list-inline-item"><a href="http://www.biodeep.cn/" target="_blank">
<img src="assets/images/[email protected]" style="height: 50px;" />
</a></li>
<li class="list-inline-item"><a href="https://panomix.com/" target="_blank">
<img src="assets/images/PANOMIX.png" style="height: 50px;" />
</a></li>
<li></li>
<li class="list-inline-item"><a href="https://bio.tools/mzkit" target="_blank">
<br />
<img src="assets/images/elixir_biotools_transparent.png" style="height: 80px;" />
</a></li>
<li class="list-inline-item"><a href="https://gcmodeller.org/" target="_blank">
<br />
<img src="assets/images/logo.png" style="height: 120px;" />
</a></li>
</ul>
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