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1. lt i pred ae Spline User demo Home Create Job View Results Stored Datasets Public Shares FAQ Account Contact Logout View Edit Dataset a x Back Add File s Delete File s Dataset ID 10352 f Name SHAM Save Reset Add Files to Dataset C FileName Active Status Size MD5 Hash Upload Date ID Cc SCIPSI_SHAM_MetOH10 mzXML zip File read OK 157 20 MB 08bfd70bc2124450acc6a28022f6b681 S 3697 X m SCIPSI_SHAM_MetOH6 mzXML zip File read OK 159 45 MB b6a07448 ja24a21252db 70120109 36948 3 m SCIPSI_SHAM_MetOH4b mzXML zip File read OK 150 17 MB b2699e894c0a13d8f11290573ca62bf R 36949 X o SCIPSI_SHAM_MetOH4 mzXML zip File read OK 193 33 MB a300abdc536a547033f8fdcc103c60 7012 0 Pi 35950 X mj SCIPSI_SHAM_MetOH16 mzXML zip File read OK 163 69MB c5197d6c70af84bed5b9967bb46c2434 ie 36951 X mi SCIPSI_SHAM_MetOH12 mzXML zip File read OK 154 20 MB 25f8128be7ca9753e32ae60d4a35bf0 2012 01 09 3695 x m SCIPSI_SHAM_MetOH11 mzXML zip File read OK 159 14 MB 4 18142c487679a150c 1e4fe2251b30f area 36953 X Page 10f1 T 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Delete Individual File from Dataset Figure 13 Edit Dataset Files All screen shots taken from v 1 22 01 Page 16 Job Sharing After you have completed an expe
2. Total lon Chromatograms original Total lon Chromatograms corrected Risteqtion Tima minutes Rananton Tins minutes Rasanton Tina minutas PNG PDF e PNG PDF e PNG PDF e Log Foki Change Plot 987 features Multidimensional Scaling Principal Component Analysis Scores Click for interactive plot to el Display additional PCA detail open in new window plots PNG PDF gt oe Complete Downloadable Results including diffreport EIC s boxplots etc results 2ip Download Full Processed Results zip Retamto Job List 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 9 Job Summary Information Interactive plot only available in certain browsers see FAQ for more information 2 Click BROWSE RESULT TABLE button Fig 9 to View Feature Details If this is the first time viewing the feature detail results of the current job the data will be loaded into the database for viewing and annotating which may cause a brief delay subsequent viewing will be faster As you navigate through each feature you can use arrow keys details about each feature m z retention time EIC box and whisker plot and putative METLIN ID s is displayed to the right of the table All screen shots taken from v 1 22 01 Pa
3. Orbitrap II UPLC G TOF UPLC UHD Q TOF View Download Results 4 Ger se of S All screen shots taken from v 1 22 01 Page 1 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 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 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 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN o x Go 7 https ixcmsonine seripps edu Bi E scrips center For metabolo x i we 93 File Edit View Favorites Tools Help fi gt Bl J mm Page gt Safety gt Toos gt gt 9 gt Scripps Center For Metabolomics XCMS Online Home Public Shares FAQ Contact News amp Updates New Version 1 22 1 New to XCMS Online Please see release notes 27 Aug 2012 Simple
4. Dataset Name Poinsot_ You are using 97 4 of your storage quota BY BE vne ronrorsonosco E hho 110240 Ema a a File List a Dataset 2 Namo Pe Osina E A Shared Fokders Uperevepre trowt Xi E J netere P debe r Detail View es 109 North Torrey Pines Road BCC 007 La Jola CA 92037 USA 858 784 9515 Fax 858 784 9496 Chrome Pr Policy Terms of Use Scripps Centar For Metabolomics Contact Us Add Files Drag to this box Figure 4 Upload Dataset Dialog en OS ger Mt All screen shots taken from v 1 22 01 Page 6 Upload Dataset 2 At this point you can repeat step number 3 to begin the second dataset upload The Dataset 2 section can be found to the right of the Dataset 1 section Note You must have unique names for each dataset even if the id is different You can modify the dataset names after an upload has started by clicking the Edit button to the right of the respective dataset name Figure 5 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN O x Go E tetps xcrsonine seripps eduljobs php acti JO A f 2 x E sores Center For Metabolo X E File Edit view Favorites Tools Help M A e Page Safety Toos lt gt Online Home Create Job View Results Stored Datasets Public Shares FAQ Account Contact Logout Job Name Dataset 1 Dataset 2 Parameters Submit
5. File Edt View Favorites Tools Help M A o ms Pager Safety Toos co G Confirm Job Specifications Job Details Coke vs Pepsi ID 119244 Coke ID 2309 Files 3 Pepsi ID 2310 Files 4 HPLC UHD Q TOF ID 2 positive Job Submit button Figure 7 Job Confirmation Dialog All screen shots taken from v 1 22 01 Page 10 View Results After you submit your job you will be forwarded to the View Results page where you can see details of your submitted jobs including progress percentage datasets used and parameter set used The page will automatically refresh if you have pending jobs however you will receive an e mail when each submitted job is complete if alerts are enabled default is to send all alerts Once complete you may view the results by clicking the green VIEW button Figure 8 You may also include publically available jobs in View Results by selecting View Public Shares from the header See Figure 8 1 Click green VIEW button on the View Results page Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN j 0 x go gt https xcmsonline scripps edu jobs php actic O alfa bedi lead Scripps Center For Metabolo X E A ke Fie Edt View Favorites Tools Hep 00000000 Tet a Bl Ol mm Page Safety Toos lt gt User demo Home Crea
6. Information is Hide or View Columns P Figure 10 Detailed Feature Information Page hyperlinked Frequently Used Features e Searching filtering is available by clicking the magnifying glass icon upper right of table e You can hide or display specific columns by clicking the icon in the lower left See Figure 10 e Clicking any column header will sort the table in ascending or descending order by that field e Column order and width can be configured by dragging and dropping column headers e Double clicking row or pressing Enter will open notes dialog box information saved in Notes column All screen shots taken from v 1 22 01 Page 13 Data Management Currently storage of user data e g uploaded datasets custom parameters and jobs results including annotations is limited See Account menu for usage To free space for additional uploads you will likely need to delete jobs and or datasets The check your account storage navigate to the Account menu See Figure 11 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN p iol x go gt https ixcmsoniine scripps edu user php acti O alfa 4t X Scripps Center For Metabolo X e 3 File Edt View Favorites Tools Help M Eo Pager Safety Toos co G mn s KEM scms Online User demo Create Job View Results Stored Datasets Public Shares Account e samt U
7. XCMS Online A Web Based Platform to Process Untargeted Metabolomic Data Analytical Chemistry 2012 If you wish to have your results added to this list you must first share the job with the public and then contact administrator use contact link with additional information e Author s e Job number e Publication citation journal link e Any notes you wish to include All screen shots taken from v 1 22 01 Page 18 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN 0 x gt gt E https lt cmsoniine scripps eduljobs php actic O Sh fa x Scripps Center For Metabolo X int Ls Fie Edit view Favorites Tools Help fh gt Gl 2 am Pager Safety gt Toos lt gt K4 User demo Create Job View Results Stored Datasets Public Shares Account View Public Shares Available Publications Count 4 Needed information for Search Jobs Search Clear publication Status ID Datasets ID control Author s Publication Notes Saghatelian et al Assignment of z WT 1022 spinal cords of 6 wild type mice and 6 112801 uez Aan Saghatelian Endogenous Substrates to Enzymes by fatty acid amide hydrolase FAAH KO 1021 Global Metabolite Profiling Biochemistry uean 2004 43 45 pp 14332 14339 4 Stone d 15027 112692 Bill Webb demo data set I beer Alesmith d 1501 Coke 1505 112691 Bill Webb dem
8. all jobs SHAM 10352 E x Public Shares Tortop Stone_IPA 970 an m 105243 Stone_vs_AleSmith 20 HPLC QT 1 x is not selected r AleSmith_IPA 971 job complete Coke 2309 105245 Coke vs Pepsi ENS HPLC Q T 258 x Pepsi 2310 EF job complete Coke 2309 E e Coke vs Peps y HPLC Q T 258 x Pepsi 2310 job complete Stone_IPA 970 1023 p Stone vs Budweiser Sea HPLC Q T 253 x Not Availabl 984 Page 1 of 1 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Select box that corresponds to job s you wish to share Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 14 Job Sharing Resubmitting When you click the Share Job s icon and new dialog box will appear on the screen where you will need to define the job sharing parameters See Figure 15 Each job may be shared multiple times with multiple users and with distinct expiration dates Figure 15 demonstrates the detail view where you define the expiration date by typing in YYYY MM DD format or selecting calendar icon and select if the job is shared with the public or a specific user You must also define if the job to be shared may be edited by your guest Upon submitting the job share dialog you will return to the View Results page and the system will automatically send an e mail to your guest inviting him her to login to th
9. 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 scree Carter For Metabo xim ia eae ex foter foo Hat fe ED mw Pger stye Toss Ge an SL Z aemet Explorer optimized os 7 Minimize JB https 7iamorine soppsedulented sokia an cf et metoder i bactionanosjit rirusmuunifredrti i114 J al fasets Storage Quota Usage 8 00 GB Select only mneXML meDote maDote XMe neted cdt d wiff Flas Moce info File Formats 2 After upload is complete reassembled m s checked this window mii autemaneaty riose Upload Compression onai oei sant z
10. mass spectrometry data processing XCMS Online featured in separationsNOW com Metabolomics for all A new web based platform for analysing LC MS data 10 Jun 2012 XCMS Online Analytical Chemistry paper XCMS Online A Web Based Platform to Process Untargeted Metabolomic Data wes published in Analytical Chemistry 10 May 2012 Current Users m aail Upload Data pa XCMS Online provides the same high quality metabolomic Cee nett analysis that you are used to but in a user friendly web g Pp based format XCMS Online allows users to easily upload Password LC MS metabolomic data that can then be processed with Select Parameters a few simple mouse clicks Predefined parameter settings for different instruments Forgot your password e g QTOF Orbitrap etc are available as well as options r for customization Results can be viewed online in an A interactive customizable table showing statistics View Download Results chromatograms and putative METLIN identities All results ZEMS Serer and images are available for download as zip files XCMS Serwer is a stand alone dedicated server for local installation More Info 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 DOWNLOAD USER MANUAL Demo login read only for testing login demo1 password 12345678 Demo datasets can be viewed using this logi
11. the parameter set you will be presented with a modal dialog box where you can define how the datasets are processed Methods and properties are available for all aspects of dataset processing See Appendix B for more details Note If you choose to change any of the settings in a template parameter set you will need to create a new parameter name for processing Figure 6 Otherwise your changes will not be saved as you can not overwrite a template parameter set The name for a custom parameter set can be set in the General tab et Explorer FATT 3 A z Ge Z hetps ijxcmsonine seripps eduljobs php action creste ORA Bi 4 x Scripps Center For Metabolo X vy Ee File Edit View Favorit es N ace Define Parameters Tools Help Polarity is defined on the General tab and will affect values on the Annotation and Identification adducts tabs Job results will be misleading if this value is not correctly defined You created a new parameter set but it will not be saved unless your click Save Current below Option Value Note Name samples Comment MyTest Parameters Retention time format minutes show the retention times in results tables and figures in minutes or seconds Polarity positive data acquired in positive or negative mode Save Current Reset Delete Close Save Custom Parameters Figure 6 View Edit Parameters for Job 5 Submit the job At this point yo
12. 5 05 2B 33 86 min 8 14 M67T14 3 115 67136 4 67 1000 13 85 46 640 whisker plot 15 M110T20_2 42 7 47639e 4 110 1000 19 83 19 432 ni 15 1 16 M8117 11 2 7 709176 4 81 1000 7 03 5 223 4 428 49 523 49 z Fi 17 M40T7 18 8 18752e 4 40 1000 7 06 32 904 175 461 322 489 38 Es 18 M97T14 3 6 8 48402e 4 97 1000 13 86 74 056 162 565 584 969 50 19 M4177 1 4 9 36524e 4 41 1000 7 07 601 600 3 856 072 5 516 855 38 F 20 M5517 1 8 4 00292e 4 55 1000 7 06 262 976 1 374 802 2 527 160 38 114 15 16 17 118 19 21 M7077 24 1 03607e 7 70 1000 7 06 298 880 1 222 973 2 991 306 38 ave 22 M87T34_2 26 5 1 242636 4 87 1000 33 88 81 536 12 553 332 936 75 23 M59T30_2 16 7 14471607 59 1000 29 67 29 224 7 274 121 632 83 55 Thymol M H 2H20 4245 24 M61T20 Infinity 1 48282e 7 61 1000 19 78 365 184 0 1 406 280 66 M 4 55 Carvone M H 2H20 34489 25 M90738 Infinity 1 554676 90 1000 37 67 34 264 0 156 803 133 M 1 5 55 2 4 7 decatrienal M H 2H20 36580 26 M101T34_2 418 0 1 80416e 101 1000 33 83 2 125 312 22 009 9 198 883 153 M 19 55 Carvone M H 2H20 41072 27 M79741 3 7 2 14396e 4 79 1000 41 24 24 312 36 468 135 140 97 55 Hesopiperitenone M H 2H20 41076 28 M54714 18 2 234006 7 54 1000 13 90 43 552 172 350 317 197 11 55 Perillyl aldehyde M H 2H20 41077 29 M84714 17 2 44581e 7 84 1000 13 90 225 600 922 284 1 375 111 11 55 Carvacrol M H 2H20 4105 i 55 Menthofuran M H 2H20 41104 55 Pinocarvone M H 2H20 T METLIN
13. Job Reset Page control You are using 97 4 of your storage quota Job Name 119244 Coke vs Pepsi Dataset 1 Dataset 2 See File Formats for more information See File Formats for more information Dataset 1 ID 2309 x Files 3 lt S Dataset 2 ID 2310 f Files 4 lt S Dataset 1 Name Coke Edit Dataset 2 Name Peps Edit Parameters Select Parameters _ Please Select Appropriate Parameter Sel T T Diemen Modify Dataset name 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 5 Screen after uploads are complete All screen shots taken from v 1 22 01 Page 7 4 Select Parameter Set After uploads are defined still in progress or complete you have to define the parameters that correspond to this job Some template parameter sets e g HPLC TOF UPLC TOF HPLC OrbiTrap have been predefined You can simply select one of those predefined parameter sets or customize them to your particular needs To begin defining parameters click on the Parameter drop down box Figure 5 After you select a template the dropdown will change and you will be able to view or edit the selected parameter set Figure 6 4a Define Custom Parameters skip this step if you do not wish to define custom parameters If you select the View Edit button to view
14. Last Update 30 AUG 2012 XCMSS 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 ElCs box plots and putative METLIN ID s 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 Upload Raw MS Data Select Parameter Set ja Li HPLC HPLC Orbitrap HPLC
15. SA 858 784 9415 Fax 858 784 9495 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 8 View Results Page All screen shots taken from v 1 22 01 Page 11 The initial results screen provides a summary of the job details replete with graphs total ion chromatograms TIC before and after retention time correction retention time deviation vs retention time log fold change bubble plot and multidimensional scaling MDS You can also download the full zipped results using the link at the bottom of the page Note This will file will not include any online annotations you input in the feature result table see next step Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN p o x Bi E X E scrips center For metabolo x iy us Si https xcmsonline scripps eduliobs php acti O File Edit View Favorites Tools Help M 2 my Pager Safety Toos ce Click to view detailed information by feature View Results Stored Datasets Public Shares Account Create Job Contact 105246 Job Name Create Date 2012 01 09 11 54 54 Parameter ID HPLC Q TOF pval 2 258 Log Finish Date 2012 01 09 13 02 11 Status job complete Total Aligned Features Experiment Type Pairwise Datasets Used Coke ID 2309 vs Pepsi ID 2310 Share Status Not Shared
16. TOF 6538 View Edit View Edit Parameters T Job Submit button 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 6 Screen after parameter selection After you click Submit Job you will have a final opportunity to view all settings for this job prior to submission A modal dialog box will appear on your screen Figure 7 with job settings Carefully review the information as this cannot be changed after submission You would need to create a new job although your data sets will already be stored If you are satisfied with the displayed information click the Submit Job button in the lower right corner of the dialog box otherwise click cancel and make the necessary changes Note It is important to not close the browser if you have uploads in progress as these will cancel There is a timer on the page that will automatically redirect the entire page to the View Results section when all uploads are complete In addition you will receive an e mail when your job has successfully queued All screen shots taken from v 1 22 01 Page 9 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN go gt https ixcmsoniine scripps edu jobs php acti O 2 G scrips Center For metabolo x E
17. e system to view the shared job You will receive a carbon copy of the invitation e mail After job is shared the shared column on View Results page will show the job is shared See Figure 8 along with a link to stop sharing the job Notes e Werecommend view only if job shared with public e Only job owner can delete job or share with guests All screen shots taken from v 1 22 01 Page 17 lee Bing and MSA 23 BE XB soveecartra teat ES Share results of your jobis accuracy Jost 4a e mail D Mow Pes Job you wil aso caa a Copy Ct he e mai Use calendar to graphically Mc ei 351 77 4 kias Data Format tyrenn select expiration date of share Select with whom you will share job results Figure 15 Job Sharing Detail Public Shares The Public Shares page is available on the top navigation menu See Figure 16 This page displays all public jobs that have publication information and have been released by administrator This section will enable academic users to publish results and reference the source experiment including parameters datasets etc Users can view filter download and analyze the raw data just like the author A user must create an account to view the results however summary information is available to general public We ask that you reciprocally cite XCMS Online when you point researchers to the public shares R Tautenhahn G J Patti D Rinehart and G Siuzdak
18. e Dataset a within dataset Figure 12 Create New Job by clicking on Create Job in the top navigation menu All screen shots taken from v 1 22 01 Page 15 Administering Datasets Clicking on the Edit View Dataset button See Figure 12 will present the dataset edit view See Figure 13 From here you can remove individual files that were uploaded as part of a dataset Simply click on the X in the far right column You may also change the dataset name or add comments to be stored with the dataset In the bottom center of screen you may add files to the current dataset by clicking the Add Files button Figure 13 Note The following actions are planned but not included in XCMS Online as of version 1 20 7 Beta e Adding the same files to multiple datasets upload once but include in separate datasets possibly as part of iterative analysis e Multiple delete files selection boxes where a user may want to delete several but not all files within a dataset e Connection to cloud storage theoretically unlimited datasets could be stored for a user or lab for indefinite period of time Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN ioj x Go gt https xcmsonline scripps edu storeddatase O alfa r X Scripps Center For Metabolo X i ve File Edit view Favorites Tools Help th gt A mm Pager Safety Tools
19. e impending action and allow you to cancel Note To rerun jobs based on deleted data you will need to re upload the data we cannot retrieve deleted datasets Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN o x go gt https xcmsonline scripps edu storeddatase O alfa 42 X Scripps Center For Metabolo X ny Le oe File Edit View Favorites Tools Help th gt Bl hy Pager Safety Toos lt gt i Acms Online User demo Create Job View Results Stored Datasets Public Shares Account Contact Stored Datasets Ps x Add Dataset s Delete Dataset s Dataset Count 13 Search Datasets Search Clear l Dataset Name Active Status Files Size Upload Date ID m SHAM UPLOAD_COMPLETE 7 1 11 GB are 10352 x oO TNT UPLOAD_COMPLETE 6 gt 9 x O 2_dataset1 UPLOAD_COMPLETE 3 528 00 bytes ee Pye i 7255 x Oo 1_dataset2 UPLOAD_COMPLETE 3 l 7254 x Oo 2_dataset2 UPLOAD_COMPLETE 3 7251 x O 1_dataset1 UPLOAD_COMPLETE 72 x m 1 UPLOADING 2 7249 x m Pepsi 4 2310 x mj Coke 3 2309 x m WT 6 1374 x E AleSmith_IPA 3 44 66 MB ery m ara D8 oO Stone_IPA 45 67 MB 6 970 x m KO 6 10 17 MB aee 765 x T Page 1 of 1 T as 07 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Click to View Edit Files blicy Terms of Use Scripps Center For Metabolomics Contact Us Delete Entir
20. ge 12 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Windows Internet Explorer Create Job View Results Stored Datasets Public Shares Account Contact Please click on a row to view feature details Feature 3 m z 115 1000 Retention Time min 33 83 Extracted Ion Chromatogram 28269 rtautenh_2012 08 01_17 41 26 1 M93T25 139 6 2 33396e 93 1000 19 640 84 045 129 M 4 2 M59T34_2 19 3 2 56736e 59 1000 33 83 28 664 7 246 139 705 s Group 1 S 2_Group 2 L 4 M42717 2 0 6 17006e 42 1000 7 06 248 256 1 239 600 2 531 535 a 5 M130T34_1 147 8 6 92196e 130 1000 33 83 55 008 1 448 213 985 202 M E 3 6 M45T34 62 2 7 787 10e 45 0000 34 02 100 648 8 578 533 601 j 7 maTo 14 3 1 42578e f 141 1500 29 88 178 880 38 585 550 727 a Ll a eee 8 M69T7 2 1 1 72069e 4 69 1000 7 06 91 664 429 275 885 745 325 330 335 34 0 345 35 0 355 B 1 258 5 2 12467e k y 121 804 j 9 m45T30_1 258 5 2 12467e 8 45 1000 29 61 21 856 440 553 804 29 1M Retention Time minutes 10 M55T14_2 1 6 3 19092e 55 1000 13 85 453 888 11 M81T41_2 3 9 4 46536e 81 1000 41 24 88 696 Switch between Mass Spectrum Boxcand wniser piot 12 M4477 1 7 4 6681 Oe 44 1000 7 06 48 032 13 m7ot25 3 4 5 12200e 4 79 1000 25 09 27 024 spectrum box and 10 0
21. ine Home Create Job View Results Stored Datasets Public Shares FAQ Account Contact Logout Job Name Dateest 4 Dataset 2 Parameters Submit Job Reset Page control Step Navigation Wizard You are using 97 4 of your storage quota Job Name 119244 kcmsonline_2012 08 27_16 03 48 Click job name to edit Dataset 1 Seg File Formats for more information See Eile Formats for more information Dataset 1 ID Not Defined T Files 0 Dataset 2 ID Not Defined Files 0 Dataset 1 Name Not Defined Dataset 2 Name Not Defined Upload Dataset 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 3 Initial job creation page All screen shots taken from v 1 22 01 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 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
22. itrap HPLC 7 Orbitrap II UPLC Q TOF UPLC UHD Q TOF View Download Results 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 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 4 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 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN ioj x s phpracti O E hy p gt lt gt Scripps Center For Metabolo X td Ue 93 File Edit View Favorites Tools Help ao phy Pager Safety gt Toos lt gt Onl
23. n but no changes can be made To nrocess datasets nlease create vour own account g Figure 1 Create user account from home page by clicking on the Register button All screen shots taken from v 1 22 01 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 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN lolx GO E https xcmsoniine scripps edu E 7 x GS Scripps center For metabolo x L AR E File Edit view Favorites Tools Help M D v Pager Safety Toos lt gt Create Job View Results Stored Datasets Public Shares Account Logout Welcome to XCMS Online Upload Raw ie D Processing LC MS data with XCMS Online is very simple ata All you need to do is to create a job which involves the two steps 1 uploading the datasets See File Formats for more information 2 selecting the parameters and submitting the job After the processing is complete you will be notified via e mail that your results are ready for review Please click Create Job to upload your datasets now or download the user manual for detailed instructions Please consult the XCMS Online forum to post suggestions feature requests and bugs Parameter Set DOWNLOAD USER MANUAL HP HPLC UHD Q TOF HPLC Orb
24. n groups e Number of missing samples to allow in retention time correction groups Note Additional options are available by clicking Advanced Options Contextual help available on site Alignment e Minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group e Allowable retention time deviations in seconds e Width of overlapping m z slices to use for creating peak density chromatograms Note Additional options are available by clicking Advanced Options Contextual help available on site Statistics e p value threshold highly significant features included e fold change threshold highly significant features e p value threshold significant features excluded Note Additional options are available by clicking Advanced Options Contextual help available on site Annotation e Search for isotopes only or isotopes adducts e m z absolute error e ppm error Identification e ppm tolerance for database search e adducts user may select multiple adducts by holding down Ctrl key Visualization e EIC width default width for ion chromatograms in seconds Miscellaneous e Other options All screen shots taken from v 1 22 01 Page 21
25. o data set Il soda Pepsi 1507 Patti et al Metabolomics implicates altered 109981 SHAM 2831 sphingolipids TNT 2830 origin Natu Page 1 of 1 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Home Change Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us Figure 16 Public Shares Resubmitting Job If you previously ran a job you may wish to resubmit the job You can resubmit a job from the View Results page by selecting the job s in the left hand and then the Resubmit Job s icon in the header See Figure 14 Number of jobs user may simultaneously resubmit may be limited by administrator Typical scenarios for resubmitting are e Job ran but one of the datasets was missing a file User would need to add files to existing dataset prior to resubmitting see Figure 13 e Job had error and did not complete the first time due to backend error Administrator would need to resolve backend issue prior to resubmitting Note If job is resubmitted and was previously successfully completed any user notes that were added to the diff report tables will be deleted All screen shots taken from v 1 22 01 Page 19 Appendix A Java Warning Dialog Security Information The application s digital signature has been verified Do you want to run the application Name jumpLoaderApplet Publisher The Scripps Research Ins
26. riment you may wish to share it with another user or the public This can be accomplished from the View Results menu You first need to select the box on the left hand side that corresponds to the job s you wish to share and then click the Share Job s icon in the header See Figure 14 Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN i 5 x S https xcmsoniine scripps edu jobs php acti O a6 4t X scripps Center For Metabolo X it s Fie Edt View Favorites Tools Help M A my Pager Safety Toos ce gt ame N Ri ick to resubmit job s XEmsS Online User demo AQ Cel ae View Jobs i i Click to share job s Create Job Resubmit Job s Delete Job s Job Count 7 Search Jobs Search Clear View Public Shares f7 Jobs sha red specifically mi Status Dy Progress JobName Datasets ID control Created Parameters ID Shared with you you are guest status H blank YC 24126 042 08 27 bgugiu_2012 08 27_16 29 22 EE Dropdown to filter job status BJAB_YC 24127 7 x a 1_Group 1 22610 ss autofilters upon selection click tautenh_2012 08 01_17 41 26 20 Remove Filter to disable and einen ed TNT 10351 Custom 201 4193 Public display GC Singl 3967 automatically even if View 2012 01 09 SHAM_vs_TNT 3 HPLC Q T 1 A display
27. ser Account Management Ye ZiR a i User Settings Parameter Manager News Manager Alerts Reporting Quota Usage Usage Breakdown t Change user interface theme Change frequency of e mail Results eee alerts job begin error Used 97 4 Active Datasets 13 7 79 GB Net ead om Active custom parameter sets 6 complete Datasets Average No files per dataset 4 0 6 23 GB Average Dataset Size 1 25 GB Total Available 8 00 GB Total Used 7 79 GB orrey Pines Road BCC 007 La Jolla CA 92037 USA 858 784 9415 Fax 858 784 9496 Total Available Storage Space ie Password Privacy Policy Terms of Use Scripps Center For Metabolomics Contact Us for jobs or datasets Figure 11 Account View All screen shots taken from v 1 22 01 Page 14 Deleting Jobs On the view results page See Figure 8 you have the option to delete a job far right column but the underlying dataset will not be deleted with a single click as you may wish to create another job with different parameters and compare results Deleting the actual datasets can be accomplished by following the steps in the section Deleting Datasets Deleting Datasets 1 Click on Stored Datasets in the top navigation bar to enter the stored datasets area This page will list all datasets previously uploaded From here you may delete the entire dataset by clicking the X in the far right column See Figure 12 A confirmation dialog box will inform you of th
28. te Job View Results Stored Datasets Public Shares FAQ Account Contact Logout View Jobs E x Share Jol z 5 Check to view others jobs Job Count 9 Click to edit job name Search Jobs Search merem m Status ID Progress J me Datasets ID controf Created Parameters ID Shared View Public Shares 7 psms ml omovies job complete WT 1022 412801 as FAAH WT vs KO ae pana HPLC Sin 2934 Public Public KO 1021 shares omplete Stone d 15027 112692 Stone vs Ale Smith HPLC Q T 2919 not Alesmith d 1501 job complete Coke 15057 2012 05 15 owned by 412691 e Coke vs Pepsi t e HPLC Q T 2919 Public Pepsi 1507 user can job complete SHAM 2831 m 109981 pere SHAM s TNT aleh HPLC Q T 2583 not TNT 2830 del job complete Sinn ete C vew 05250 SHAM_ys_TNT Click to stop sharing this job Stop with all guests sharing Stone_vs_AleSmith AleSmith_IPA 971 ai A Coke 2309 2012 01 09 View Job Results Only available Coke vs Pepsi Som 145454 HPLC Q T 258 epsi when button is green Coke 2309 Coke vs Pepsi 2011 0 HPLC Q T 258 x x x ne Pepsi 2310 job complete Stone_IPA 970 uyn PEE r hee eee 2011 05 12 xpic Click X to delete job Note will dia Not Avallabl 034 not remove datasets see section Page 1 of 1 Deleting datasets 10550 North Torrey Pines Road BCC 007 La Jolla CA 92037 U
29. titute From https xcmsonline scripps edu your personal information at risk The publisher s identity has been More Information EJ This application will run with unrestricted access which may put verified Run this application only if you trust the publisher Figure A1 Java Warning Dialog All screen shots taken from v 1 22 01 Page 20 Appendix B Custom Parameter Creation If you wish to create custom parameters for your experiment you will need to create a job following the steps described in the quick start guide Once you elect to create your own parameter set you will want to modify the default properties of a pre defined parameter set Step 4a Each tab has categorized information for how XCMS Online will analyze your datasets Tab Options Available General e Job Name Comment e Retention time format minutes or seconds e Polarity positive or negative Feature Detection Choose method CentWave or matchedFilter CentWave e PPM e Minimum Maximum peak width matchedFilter e FWHM full width at half maximum of matched filtration Gaussian model peak e Step size to use for profile generation Note Additional options are available by clicking Advanced Options Contextual help available on site Retention Time Correction Choose method obiwarp peakgroups or none Obiwarp Step size PeakGroups e Linear or non linear alignment e Extra peaks to allow in retention time correctio
30. u can review all relevant details about the job prior to submission e g job name dataset names correct file count correct parameters Once you are satisfied click the Submit Job All screen shots taken from v 1 22 01 Page 8 button to queue the job for processing The Submit Job button can be found at the bottom of the screen Figure 6 Note Even if you still have datasets uploading you can pre submit the job so it will automatically queue once the datasets complete the upload Scripps Center For Metabolomics and Mass Spectrometry XCMS Online Internet Explorer optimized for Bing and MSN lol xj g9 https xcmsonline scripps edu jobs php acti O alfa 47 X scripps Center For Metabolo X Li M i amp Fie Edit view Favorites Tools Help A o mo Pager Safety Toos gt ce Gb gt al Saline User demo Home Create Job View Results Stored Datasets Public Shares FAQ Account Contact Logout Job Name Daseri Dataset 2 Parameters Submit Job Reset Page control You are using 97 4 of your storage quota Job Name 119244 Coke vs Pepsi Dataset 1 s See File Formats for more information See File Formats for more information Dataset 1 ID 2309 v Files 3 w Dataset 2 ID 2310 w Files 4 w Dataset 1 Name Coke Edit Dataset 2 Name Peps Edit Hac I UHD Q TOF a optimized for HPLC with 60 min gradient high resolution ESI QTOF MS e g Agilent UHD Q

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