代谢组学软件：xcms usermanual

All screen shots taken from v. 1.22.01. Page 1 Last Update: 30 AUG 2012 XCMS Online Usage Instructions Overview XCMS Online is an innovative platform with an intuitive graphical interface which allows users to easily upload and process LC/MS data for untargeted metabolomics profiling. XCMS Online provides a complete metabolomics workflow including feature detection, retention time correction, alignment, annotation and statistical analysis. To facilitate the usage, predefined parameter sets for different instrument setups (e.g. HPLC/QTOF, UPLC/QTOF, HPLC/Orbitrap) can be selected. Customized settings can be created from these templates. Results can be browsed online in an interactive, customizable table that shows feature statistics, EICs, box plots, and putative METLIN IDs for each metabolite. All results including the images may also be downloaded as a zip file for offline analysis. You will need a user account to use the system however user accounts are free and only require a valid e-mail address to register. To process datasets using XCMS Online you will need to create a job which involves uploading the datasets, defining parameters and submitting the job. You will be notified of your job status, including errors/warnings that you can correct prior to resubmitting a job. After processing is complete, you will be notified via e-mail that your results are ready for review. All screen shots taken from v. 1.22.01. Page 2 Table of Contents Quick Start Guide 3 Uploading Datasets 5 Define Parameters 8 View Results 11 Account Administration 14 Dataset Administration 15 Job Sharing 17 Public Shares 18 Resubmitting Jobs 19 Java Warning Dialog Screenshot Appendix A Custom Parameter Creation Appendix B All screen shots taken from v. 1.22.01. Page 3 Quick Start 1. Create User Account You will initially need to register your e-mail account to be able to use the system. After you register you will receive an e-mail at the account you entered with validation instructions. Upon validation you will have access to the system. You may then login using the username and password combination you used to register. Figure 1 Create user account from home page by clicking on the “Register” button All screen shots taken from v. 1.22.01. Page 4 2. Create Job As a first-time user, you will want to begin by creating a new job. Click on “Create Job” in the top navigation menu (Figure 2) Figure 2 Create New Job by clicking on “Create Job” in the top navigation menu All screen shots taken from v. 1.22.01. Page 5 3. Uploading the Datasets - The create job page will open and you will be able to start defining the job (see Figure 3). There is a step navigation wizard directly below the top navigation bar that will serve as a guide. Upon initial load, a default job name will be created based on your user name and the current date. You may click the job name to edit. Upload Dataset 1 Initially you will need to upload a dataset. Dataset 1 (left-hand side) is often defined as the control data set. a) Click the “Upload Dataset” button to initiate an upload. A separate window will open. This will load the Java module which is required for large uploads. Even if you receive a warning (see Appendix Figure A1), click “Run”. After the applet runs, you will be presented with an upload dialog box (see Figure 4). Figure 3 Initial job creation page Step Navigation Wizard Click job name to edit Upload Dataset All screen shots taken from v. 1.22.01. Page 6 b) Select files/folders to be included in the dataset from the file tree (Figure 4). Individual files will appear in the file list as you navigate the file tree. After you locate the files for this dataset, drag them to the “Drop Files Here” area (lower-right) and they will immediately start compressing. Alternatively you can click the “+” symbol (see “Add Files” in Figure 4) to select the files you want to include. When you are satisfied all files are included in this dataset, you may press the “Upload” button to start the upload. You may need to maximize window size or use scroll bars to display all text. The animated line under a file or folder appears during file zipping. You may need to wait until zipping finishes prior to clicking the upload button. Note: Valid files the system can accept include mzXML, mzData, mzData.XML, netCDF, wiff (AB SCIEX), CDF and folders with “.d” extension (Agilent) at present. Additional formats may be included in future versions. c) Depending on the speed of your Internet connection, you may choose to continue with the job setup. At this point you can minimize the upload in progress and continue. Alternatively you can drag the upload dialog box to another part of the screen so you can access the main create job page. Simply use the minimize button (single bar) in the upper right-hand corner of the window (See Figure 4). Note: minimize button may be different depending on operating system. Note: If you close the dialog box, you will need to start again.