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Chembiodraw里的Fragmentation Tool可以用于质谱图的预测分析吗已有2人参与
我需要先用标准品做质谱，用的是LC-MS/MS QQQ质谱仪，需要对样品的碎片进行一些简单分析，例如碎片的断键方式之类。请问Chembiodraw里的Fragmentation Tool断裂预测可以用于辅助解析吗？有什么需要注意的地方呢？
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应该是不行的。它模拟的是EI源的碎片断裂，LC-MS都是软电离源，我估计你用的八成是ESI，是模拟不出来的。
雲幕低垂映桂子，江月留白問柳心。
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【悬赏金币】回答本帖问题，作者Cydta将赠送您 5 个金币
(初入文坛)
在线: 12.9小时
虫号: 2857001
注册: 专业: 生物大分子结构与功能
Chembiodraw里的Fragmentation Tool可以用于质谱图的预测分析吗已有2人参与
我需要先用标准品做质谱，用的是LC-MS/MS QQQ质谱仪，需要对样品的碎片进行一些简单分析，例如碎片的断键方式之类。请问Chembiodraw里的Fragmentation Tool断裂预测可以用于辅助解析吗？有什么需要注意的地方呢？
& 猜你喜欢
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【答案】应助回帖
感谢参与，应助指数 +1
那个软件模拟的原理，是基于EI源的原理，液质会有偏差。
我那么努力，就是为了在更高的层次遇见你！
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引用回帖:: Originally posted by Cydta at
那液质分析用什么软件比较好呢？我主要是想确定碎片离子中的碳位顺序，比如说A碎片是母离子中的2、3、4碳位，B碎片是母离子中是2、3、4、5碳位。我是小白，还请多多赐教呢... 液质分析的话，各个公司的仪器，都会有自己的数据处理软件。都是随着仪器成套买的。
我那么努力，就是为了在更高的层次遇见你！
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ChemBioDraw Ultra 14.0 Suite
The ChemBioDraw Ultra 14.0 suite provides scientists with an up to date collection of scientifically intelligent applications for chemical structure drawing and analysis combined with biological pathway drawing.
Highlights in ChemBioDraw 14.0 Ultra
Search SciFinder direct from ChemBioDraw Ultra with no time-consuming cutting and pasting.
Copy and paste CDXML and molfile text to and from the clipboard for data exchange with other applications that can consume these file formats.
Biopolymer toolbar with disulfide and lactam bridges, beta and D-amino acids, DNA, RNA, protecting groups and linkers
Paste peptide, DNA and RNA sequences and have them interpreted chemically with sequence wrapping and shaping
Gel Electrophoresis Plate Tool provides arbitrary rotation for lane labels, drag and position band labels, paste data from Excel or other sources, and copy and paste between lanes
Calculators for pKa*, LogP and LogS* enable scientists to explore important bioavailability properties such acid dissociation, distribution and aqueous solubility for putative compounds
*Windows only
Figure 1: Image showing the electrophoresis plate, biopolymer sequence and 3D structure.
(W = Windows Only)
Applications Included
ChemBioDraw Ultra
This ultimate chemistry and biology drawing application delivers all of the industry leading drawing, publishing and analytical features in ChemDraw combined with the biology features in BioDraw, providing a complete solution for chemical structure drawing and analysis combined with biological pathway drawing.ChemBioDraw Ultra chemical structure analysis tools include 13C and 1H NMR prediction with peak splitting and highlighting and choice of solvent, Struct=Name, ChemDraw/Excel, stoichiometric analysis, property predictions including pKa, LogD and LogS live-linked to the structure, a live-linked Database Gateway, fragmentation tools, TLC and Gel Electrophoresis plate drawing tools, and 3D structures live-linked to the 2D structure. ChemBioDraw also offers customization options for Nicknames, Templates, and HotKeys, and adds a new Save to Dropbox feature. A new biopolymer toolbar enables creation of peptide, DNA and RNA sequences, including beta and D-amino acids, disulfide and lactam bridges and linkers and protecting groups. Biological pathway drawing elements include membranes, DNA, enzymes, receptors, and reaction arrows. tRNA, Ribosomes, Helix Proteins, Golgi Bodies, G-Proteins, Immunoglobins, Mitochondrion, new Freehand Pen Tool, Annotation, and a Plasmid mapping tool are also included.
Chem3D Pro
This premier application for desktop molecular modeling and protein visualization provides support for state-of-the-art open GL graphics and stereo hardware. Build small molecules using the ChemDraw interface and see the 3D structure appear simultaneously, perform basic Molecular modeling computations such as Dihedral driver MM2 experiments, Molecular Mechanics and Dynamics. Perform ab initio calculations with an interface to GAMESS.
ChemBioFinder Ultra
ChemBioFinder Ultra is the ultimate database management system for chemical structure and information databases. Browse, create, search, and update local databases with structural, numeric, and text data via user-customizable forms, including structural, sub-structural, and similarity queries, as well as linking to related data in sub-forms. Calculate values for physical properties, view and edit structures in a variety of modes, automatically create databases and forms for imported data, export and print. Easily manage saved queries, access favorite databases, and view database structure via the dockable Explorer Window. Features include the ability to perform RGroup Analysis, read graphic files from the database, Python programming and improved tautomeric searching.
ChemBioFinder for Office
ChemBioFinder for Office locates and searches structure files contained in documents on your computer or network drives. Multiple structure file types are recognized, including cdx, mol, sdf, rxn and skc, and search results can be displayed or exported as SDfiles.
ChemBioViz Pro
ChemBioViz Pro is a rich toolkit for visualizing numeric data in ChemBioFinder. Calculate and display structure activity relationships, clustering relationships, and statistical data, including histograms, scatter, logarithmic plots, and dendrograms. Descriptive statistics include minimum, maximum, mean, median, standard deviation and more. Create Compound Profiles and visually compare and rank structures based on values of selected properties and the cost profile associated with each property. Create plots within ChemBioFinder sub-forms.ChemBioViz is a visualization application which works with ChemBioFinder Ultra and allows users to correlate biological activity with chemical structures. ChemBioViz transforms ChemBioFinder data into easy to understand graphics, allowing scientists to easily discern structure-activity relationships. ChemBioViz generates an interactive window containing a variety of plot types and allows researchers to analyze data using a variety of statistical analytical tools. Users can then filter their data on any field in the database in order to examine subsets of data in order to locate trends and correlations.
ChemDraw/Excel Pro
ChemDraw/Excel allows scientists to create chemically intelligent spreadsheets within the familiar Microsoft Excel environment. Build and manipulate chemical structures within Excel, compute chemical properties and use structure and substructure searches to locate and group compounds.
BioDraw Ultra
BioDraw Ultra makes drawing and annotating biological pathways quick and straightforward, adding an unmatched level of uniformity and detail. Drawing elements include membranes, DNA, enzymes, receptors, and reaction arrows, tRNA, Ribosomes, Helix Proteins, Golgi Bodies, G-Proteins, Immunoglobins, Mitochondrion and a Plasmid Map Tool. BioDraw Ultra now includes a biopolymer toolbar for drawing and editing peptide and nucleotide sequences using single and three letter codes, including beta and D-amino acids. The sequences can be expanded and contracted and sulfide and lactam bridges can be easily added.
ChemNMR Pro
ChemNMR can be used to accurately estimate 13C and 1H (proton) NMR chemical shifts. The molecule and the spectrum appear in a new window. The chemical shifts are displayed on the molecule and the spectrum is linked to the structure so that clicking on a peak in the spectrum highlights the related fragment on the molecule. With ChemNMR 13.0, the solvent can be specified as DMSO or CDCl3.
Struct=Name Pro
Struct=Name contains the leading comprehensive methods for converting chemical structures into IUPAC chemical names and names to structures. It can be used for many types of compounds, including charged compounds and salts, bridged and fused ring systems, highly symmetric structures, isotopically labeled compounds and many other types of inorganic and organometallics.
MestReNova Std/Lite
MestRe Nova (MNova) Std is a 1D only application for data processing, visualization and analysis of NMR data. The program provides a variety of conversion facilities for most NMR spectrometer formats and includes the conventional processing, displaying and plotting capabilities of an NMR program, and more advanced processing techniques. MNova Std/Lite is a 1D only version of MNova which offers the user basic processing and analysis capabilities. The full version of MNova is available through the SciStore online store or directly through Mestrelab Research.
Applications Features
(W) – Feature available on Windows only
ChemBioDraw Ultra
ActiveX Edit in ChemDraw
Edit your document using your installed version of ChemDraw, rather than your ActiveX, providing greater screen real estate for editing, and also access to the full range of ChemDraw capabilities.
Arrows Tool
Control every aspect of arrows drawn, including arc, length, headstyle, dipole, no-go and more.
Draw biological pathways.
Biopolymer Toolbar
Draw peptides and nucleotide (DNA, RNA) sequences using 1- and 3- letter codes. Includes natural L-, unnatural D- and beta amino acids. Simply switch between 1- and 3- letter codes and expand and contract labels. Insert linking and protecting groups with simple type-ahead functionality. Use the bond tool to create disulfide and lactam bridges, and cyclic peptides.
Chain Tools
Draw both acyclic and snaking chains.
Chem3D HotLink
(W) See what structures look like in 3D in a floating window and open Chem3D with a single click from within ChemDraw.
Chemical File Format
Reading & writing of chemical file formats including skc, mol v3000, sdf, spectra & reactions.
Chemical Warnings
Mouse-over red box to read error description.
Users can now select whether they want the spectrum predicted in CDCl3 or DMSO.
ChemNMR User Proton Shift Database
Users can add their own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.
(W) Advanced property parameter including BP, MP and more.
CLogP/CMR provides the latest methodology for calculationg n-octanol/water partition coefficients and molar refractivity.
Custom Templates & Nicknames
Ability to create & edit templates & nicknames
Database HotLink
Search PerkinElmer Informatics databases for chemical structures in real time as you draw.
Expand Generic Structure
Generate multiple structures from an “abbreviated” generic structure.
Floating Character Map
Add special characters from any font instantly to any ChemDraw document.
Floating Periodic Table
Element information available at all times with floating periodic table on the desktop.
Freehand Drawing Tool
Use the mouse or other pointing device to draw freehand shapes using this intuitive drawing tool.
Gel Electrophoresis Plate Tool
Draw gel electrophoresis plates. This new tool is similar to TLC Plate Tool, and provides arbitrary rotation for lane labels, drag and position band labels, paste data from Excel or other sources, and copy and paste between lanes.
High Colour Documents and Templates
Documents can contain over 16 million colors. Create high color pathway and element templates.
I/Draw Mode
New compatibility mode allows ChemDraw to look and feel like your legacy drawing package.
ISIS-style Data SGroups
Data can be attached to objects.
Publication-quality EPS glassware art for use within your ChemDraw documents.
Calculate the logarithmic value of the distribution coefficient D, which is the ratio of the sum of the concentrations of all forms of the compound (ionized plus un-ionized) in each of the two phases.
Calculate the logarithmic value of the aqueous solubility S of a compound. This value significantly affects its absorption and distribution characteristics.
Mass & Other Fragmentation Tools
Three fragmentation tools: Mass, Dissociation, & Retrosynthesis.
MS Office Integration
(W) ChemDraw offers full integration via OLE, so you can embed your drawings in any Office document.
Multi-Page Docs
Create multiple page documents and posters within a single ChemDraw file.
Name=Struct
Produce structures from systematic and common chemical structure names, and generate systematic IUPAC names from structures. Works for many types of compounds, including charged compounds and salts, isotopically labeled compounds, highly symmetric structures and many other types of organic, inorganic and organometallics.
Online Menu
(W) Draw a structure or model and immediately get online vendor information ChemACX.Com with the click of a button.
Paste Sequences
Paste sequences in FASTA format. Copy a text string describing a biopolymer as a series of single or multi letter residues, with valid separators (space, tab, dash), and paste it as a sequence with full chemistry.
Calculate the logarithmic value of the acid dissociation constant Ka, which is a quantitative measure of the strength of an acid in solution.
Plasmid Map Tool
Create a plasmid map entering the number of base pairs in the plasmid map and specifying ranges for regions and locations and labels for markers.
Polymer Draw
Represent and manipulate polymers in ChemDraw.
Properties HotLink
Chemical names, formulas, molecular weights, and other physical properties added to the document are “live”, and will now update automatically as modifications are made to structural diagrams.
Relative Stereochemistry
Allows specification of relationships between groups of stereocenters smaller than an entire molecule.
Rotation about Arbitrary Centres
Change the center of rotation using adjustment handle on the Lasso and Marquee tools. Rotation will now be centered on the selected origin.
Save to Dropbox
Use Cloud storage via Dropbox to save, share and import ChemBio3D models in a secure but sharable Cloud location.
Sequence Tool
Draw peptide or nucleotide sequences using using 1 and 3 letter codes. The atoms are labeled with amino acid or nucleotide nicknames. The sequences can be expanded and contracted.
Stereochemistry
Identifies stereocenters using Cahn-Ingold Prelog rules.
Stoichiometry Grid
Automatically track and update stoichiometry data for any user-defined chemical reaction.
Structure CleanUp
Improves poor drawings.
Structure Perspective Tool
Adjust the perspective of ChemDraw molecules with simple horizontal/vertical mouse movements.
TLC Plate Tool
Draw thin layer chromatography plates. Drag plate to size and drag spots to required positions. Shape and color spots and set or display Rf values.
Topological Polar Surface Area (tPSA) provides a fast approximation of the molecular polar surface area, a useful parameter for prediction of drug transport properties, which has been show to correlate with human intestinal absorption and blood-brain barrier penetration.
Chem3D Pro
(W) Advanced property parameter including BP, MP and more.
Dihedral Driver
(W) New conformational analysis tool allows the generation of MM2 energy plots.
Enhanced Graphics
(W) Chem3D uses openGL to provide high quality graphics display.
Group Labels
(W) Display group labels in the Chem3D model view.
Hydrogen Bonds
(W) Automatically display hydrogen bonds in the 3D view!
Kekule/Delocalised Display Mode
(W) Toggle between dashed line and alternating single-double bond representation of delocalised and aromatic bonds.
(W) Built in support for MM2 to generate realistic 3D structures.
Model Explorer
(W) Hierarchical tree-control for exploring the structure of large models. Import a PDB file and examine chains, groups, and ligands. This new feature gives fine-grained control.
Molecular Modelling & Dynamics
(W) Workstation quality molecular modelling.
Multiprocessor Support
Enable multiprocessor support in MMFF94 calculations.
PowerPoint
(W) Embed Chem3D models in PowerPoint files. Rotate and zoom Chem3D models while giving a presentation.
Spectrum Viewer
(W) Display spectral calculation results from Jaguar, Gaussian, and GAMESS as a graphical display in a separate window.
ChemBioFinder Ultra
3D Query/Finder
(W) Query ChemFinder database by 3D parameter.
ActiveX Control Boxes
(W) Include third party ActiveX controls on your form.
Automatic Form Generation
(W) Automatically build or extend databases by importing structures from collections of structure files, databases, SDFiles, or other sources.
ChemBioFinder/Office
(W) Search on your computer or network for chemical structures in Word, Excel, Powerpoint, ChemDraw, ISIS files and more, and browse, search, refine, or export your hit list to any destination.
ChemBioViz
(W) The bio visualization add-on to ChemBioFinder allows you to create graphical representations of ChemBioFinder databases in order to identify trends and correlations within subsets of your data.
Chemical Searching
(W) Search for (sub)structure, similarity, numeric values, text, chemical formula (including element ranges, element exclusions), date. Support for tautomers and alt groups.
Clustering Analysis
Discover similarities within sets of compounds and properties.
Compound Profiles
(W) Visually compare and rank structures based on values of selected properties and the cost profile associated with each property.
Hit List and Query Management
(W) Use a navigation tree to track history of searches between sessions, allow queries to be re merge lists by drag-and-drop in tree. Queries color-coded to relate to ChemBioViz plots.
List Merge
(W) Merge hitlists with any logic: intersect, union, subtract, reverse subtract.
Multiple Data Views
(W) View records one at a time, in a table view or a multiform view.
(W) Plot one or two variables with a variety of plotting options. Hover over a point to view the corresponding chemical structure. Filter displayed points by any numeric variable using a slider control.
Plotting: Statistical Analysis and Customisation
(W) Perform statistical analyses and display the results on the plot, modify the shape and colour of plot points, add comment boxes, change axis label text and background colour.
Plotting: Subform Plots
(W) Include miniature plots inside subform boxes for quick visualisation of subform data on a per-compound basis.
Property Generation
(W) Generate many types
populate database fields automatically or generate on-the-fly per record.
Python Scripting
Python scripts can be written to automate the application and can be attached to buttons on the form or to database trigger events. User the enhanced Script Editor to develop and debug — now featuring interactive line-by-line execution — and display output in a new dockable text window.
(W) Python scripts can be written to automate the application and can be attached to buttons on the form or to database trigger events. User the enhanced Script Editor to develop and debug — now featuring interactive line-by-line execution — and display output in a new dockable text window. CAL is a simple programming language, accessible to non-programmers allows automation, self-running demos, includes debugging features.
Standardized Handling of Implict Hydrogens
Conforms to industry standards.
(W) Link relational data to your main table via subforms.
Tabbed Forms
(W) Partition a form into sections using tabbed form pages.
BioDraw Ultra
Arrows Tool
Control every aspect of arrows drawn, including arc, length, headstyle, dipole, no-go and more.
Chain Tools
Draw both acyclic and snaking chains.
Chemical Warnings
Mouse-over red box to read error description.
Expanded Generic Structure
Generate multiple structures from an “abbreviated” generic structure.
Floating Character Map
Add special characters from any font instantly to any ChemDraw document.
Floating Periodic Table
Element information available at all times with floating periodic table on the desktop.
Freehand Drawing Tool
Use the mouse or other pointing device to draw freehand shapes using this intuitive drawing tool.
High-Colour Templates
A set of high color pathway and element templates.
Mass & Other Fragmentation Tools
Three fragmentation tools: Mass, Dissociation, & Retrosynthesis.
MS Office Integration
(W) ChemDraw offers full integration via OLE, so you can embed your drawings in any Office document.
Plasmid Map Tool
Create a plasmid map entering the number of base pairs in the plasmid map and specifying ranges for regions and locations and labels for markers.
Polymer Draw
Represent and manipulate polymers in ChemDraw.
Properties HotLink
Chemical names, formulas, molecular weights, and other physical properties added to the document are “live”, and will now update automatically as modifications are made to structural diagrams.
Relative Stereochemistry
Allows specification of relationships between groups of stereocenters smaller than an entire molecule.
Sequence Tool
Draw peptide or nucleotide sequences using using 1 and 3 letter codes. The atoms are labeled with amino acid or nucleotide nicknames. The sequences can be expanded and contracted.
Stereochemistry
Identifies stereocenters using Cahn-Ingold Prelog rules.
Structure CleanUp
Improves poor drawings.
Structure Perspective Tool
Adjust the perspective of ChemDraw molecules with simple horizontal/vertical mouse movements.
TLC Plate Tool
Draw thin layer chromatography plates. Drag plate to size and drag spots to required positions. Shape and color spots and set or display Rf values.
ChemDraw/Excel Pro
ChemDraw/Excel
(W) Use Excel to organise and analyse your chemical data.
Name=Struct/Excel
(W) Generate a ChemDraw structure in MS Excel by typing in systematic chemical names for most substances.
ChemNMR Pro
Predict Proton NMR spectra with splitting patterns. Also predict Carbon-13 NMR spectra. Spectra and peaks are linked to the structure for clear interpretation. Add your own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.
ChemNMR User Proton Shift Database
Users can add their own shift correction data for proton prediction which can supplement the existing data used by the ChemNMR algorithm.
Struct=Name Pro
Name=Struct
Produce structures from systematic and common chemical structure names. It can be used for many types of compounds, including charged compounds and salts, highly symmetric structures and many other types of organic, inorganic and organometallics.
Struct=Name
Produce names for many more types of compounds, including charged compounds and salts, highly symmetric structures, many types of inorganic and organometallic compounds and others.
MestRe Nova Std/Lite
1D NMR Processing
Process and analyze 1D NMR FID (free induction decay) files.
System Requirements
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