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1、All screen shots taken from v. 1.08Beta (actual screens will be similar however design modifications may be made in subsequent versions). Page 1 Last Update: 21 JUL 2011 XCMS Online Usage Instructions Overview XCMS Online is a new platform with an intuitive graphical interface which allows users to
2、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 i
3、nstrument 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 r
4、esults including the images can also be downloaded as 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 through the XCMS Online system you will need to create a job whi
5、ch 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. A
6、ll screen shots taken from v. 1.08Beta (actual screens will be similar however design modifications may be made in subsequent versions). Page 2 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
7、 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 sho
8、ts taken from v. 1.08Beta (actual screens will be similar however design modifications may be made in subsequent versions). Page 3 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
9、clicking on “Create Job” in the top navigation menu All screen shots taken from v. 1.08Beta (actual screens will be similar however design modifications may be made in subsequent versions). Page 4 3. Uploading the Datasets - The create job page will open and you will be able to start defining the jo
10、b (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 up
11、load 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. This will load the Java module which is required for large uploads. Even if you receive a warning (see Appendix A Figure A1), click “Run”. After the applet
12、 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. 1.08Beta (actual screens will be similar however design modifications may be made in subsequent versio
13、ns). Page 5 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 s
14、tart 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. The animated line under a file or folder appears d
15、uring 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,CDF and folders with “.d” extension (Agilent) at present. Additional formats may be included in future versions. (See
16、 Appendix B for more information) 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. The yellow minimize button can be found in the upper-left corner of the upload dialog (Figure 4). Note: If you close the dialog box, you will need to st
