ShiftedIonsFinder 1.1.6 User`s Manual (English)
Contents
1. ii iii 33333333333333 8 When Not Using PovverGet cccccccccccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 8 lt Memory Setup and Startup 9 s Memory ub b b m b m b bar 9 Starting Up ShiftedlonsFinder for a Windows User 9 Starting Up ShiftedlonsFinder for a Macintosh User 2 9 zocreeh C ongure a m m 10 Configuration of Main Frame 2 10 Configuration of Menu Bar 222 10 Configuration of Data Display Tab Panel 2222 11 lt Import Data TPU onines a aa AN 12 12 lt Management of Element 14 Editing Element Data 22 14 Audmne Element Dy at aH so 15 Deleting Element Data 16 lt Search Conditions 17 Setting the Element Data 0 0 0 0 ccc ccccccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeees 17 oetting the mada maa maa Bay 17 Tocunulucu lub b b b b b b sabi 17 ociuno HER CDI d aad 18 lt Search Execution and Sea2. aetisl 22 5367958 190 9119 188 9046 1200511 Adua 0 0 00091613 00000160 5 350786 1909119 1899047 7065372 tal 2 5 369979 274 0732 205 0705 1207453 Actua 0 0 90060405 0 0000131 5 362030 2748732 205 3705 71499 69 Actual 24 5 309234 270 8713 2073766 2586333 0 0 20024675 00000039 5 300163 2768713 207 8700 14066 04 Actual 25 5 373326 356 8345 239 8398 71864 28 Actual 0 0 00064054 0000009 5 264920 358 8345 289 8398 39070 28 Actuals 26 5 375187 444 7940 3757991 2238114 Actual 0 0 00097299 0 5 365447 4447939 4417866 3381185 27 5 375724 360 8326 281 6379 19045 75 Anua 0 00117622 363862 360 8326 2918379 8309 707 Actual 28 4427950 37320911 61507 44 Adua 0 0 0 0063967 0 0000316 5 369694 4427956 3739011 31189 17 Actual 29 3 379739 126 0767 15 0005 8874244 Adua 1 9 00116201 0 0000035 5 368113 1010935 400 0802 25408 41 Actuale 30 5 381050 520 7571 525 7498 6000239 Adua _ 1 0 00089971 00000030 5 372053 5267571 4577624 2049400 factual _ 31 5 381969 610 7184 541 7237 33829 71 Actual 0 0 0 0099076 00000402 5 372061 510 7184 5417237 15756 57 Actual 32 525 7551 459 7506 2357443 Adua 1 0 00140332 00000401 5369060 528 7552 459 7605 1180693 Acil 46 5 394936 209 1050 206 0977 15417 44 Actual 0 0 90118485 0 0000057 5 383006 209 1050 206 977 13032 83 Actual
3. 1 406231 876 5767 877 5295 2880842 Acual _ 49 6 00190440 00000244 06 2289 5 389187 8785767 877 5694 7015448 Aciual 85 5 400504 712 6518 771 6445 38400 45 Actual 5 0 0 0189768 00000523 00723479865 5 3090257 7126518 7116445 11184 35 Actual a4 5438715 227 1156 226 1092 1255732 Atusi 1 0 02205071 00006452 28408 95 5 669242 2271163 226 1090 1458582 jadual 1 100 5 477951 175 1188 174 1116 1727408 Actual ves 1 5 00117247 90000394 02187240862 5 465226 180 1357 179 1284 20915 44 Actuals miz Oit RT Dat oz 2483490 180 0860 179 0793 4780190 Adua 1 98031400 0 0000439 0237104712601 5 291030 1851034 107 0000 1012089 cw 110 5 580001 140 0812 144 0739 2024477 Actual 1 5 0 7058913 00000015 040446728 254 5 285052 181 0979 140 0904 17918 44 fActuale r ae am 1 START x 20 r 0 ana n ADATAS Mici 4 1 Column that displays the information of the basic sample that was hit in the search If there are multiple hits the same information is displayed in different rows since a row is created for each hit 2 Column that displays associated information 3 Column that displays the information of the shifted sample that was hit in the search 20 lt Join the search result gt The Join function combines into a table the multiple search results in which the same basic sample is used Thus you
4. 2 1829249 121 9172 1983122 Acua yes 0 00102933 0 0000109 53815637 1229245 1219172 1020706 cwale yes 53 5 308771 124 9226 1239153 2864370 yes 0 0 00171119 0 0000032 0 026615 5 481850 12492266 1230151 1410510 yes 54 5399768 207 8892 206 6819 1403493 Actual r _ 0 0 0193267 0 0000100 5 300431 207 6892 206 8819 5318689 Avales 56 5 400091 2945434 2926361 2042030 Actual 0 0 00169520 0 0000450 0 15 5 383109 2949433 2935350 7912107 ectu l 58 5400328 206 8358 2058785 75401537 Acual yes 0 1 0 0203274 0 0000306 5360431 207 8892 2066819 5318689 ual 58 5400428 206 8858 2068785 75401537 Adual yes 9 0 00192521 1010000047 0022 5 301576 206 8868 206 8786 3469223 duals Yes 50 5 400896 208 8840 207 8767 1568122 Actual 0 0 0138404 0 0000180 0086172 5 38205 208 8840 207 8767 71057 78 Acuale 5 5401503 201 0887 200 0815 2716530 ez 2 0 0 0200246 0 0000061 5 381579 2010887 200 0815 25919 26 2 5401700 290 8471 28986398 7158109 5 0 0 90181236 00000049 5 383575 2905471 289 6396 3057756 5401897 2926453 2918380 1986998 yes 0 0 00186529 0 0000175 0 5383254 2928452 2918380 4345565 66 5 402253 460 7678 459 7608 80075 58 1 0 00142170 0 0000712 5 388036 460 7678 459 7606 2975382 s7 5646 7271 545 7109 1726365 Attuali 0 0 0
5. hiftedlonsFinder Version 1 1 6 User s Manual lt Introduction gt In mass spectrometry based metabolomics it is important that the elemental composition is estimated from the accurate mass values of all the detected peaks and that the annotation of a compound is performed by comparing its analytical data with that of authentic chemicals or compounds in public databases However when the intensity of a detected peak is not within an appropriate range a deviation error from the accurate mass occurs and it may not be possible to estimate the elemental composition accurately This problem tends to occur in particular when analyzing biological samples because the quantities of the compounds contained in a sample differ widely A technique for solving this problem is to label the biological sample externally with a stable isotope and estimate the elemental composition at a very reliable level using as an index the number of stable isotopes incorporated in the compound The ShiftedIonsFinder is an analytical tool GUI program for finding peaks having specified mass differences by comparing the mass spectra in two data sets obtained using chromatography accurate mass spectrometry This tool enables the user to select candidate labeled peaks by comparing a sample that is externally labeled with a stable isotope with an unlabeled sample It is also easy to select peaks that may have been modified by hydration glycosylation or acylation Since th
6. unit or ppm button unit ppm 17 Setting the RT Dif In the search conditions setup panel enter any value in the RT Dif box It is set to 0 3 by default but an appropriate value must be entered depending on analysis conditions such as the chromatography conditions RT Dif 18 lt Search Execution and Search Results Format gt In this section we describe how the search is executed and how to read the search results Search Execution Method After the required setup is complete start the search process by clicking the Start button in the search conditions setup panel When the process is started a dialog that shows the state of progress is displayed Start xt Shifted Shoot_13C_labeling bd a3 01 tab panel The flow of the search including setup and related functions performed to this point 1s shown below Importing of import data Selection of element data Setting Max Fold l Setting m z Dif Setting RT Dif Start of search by clicking the Start button l Display of search results data on result the name of selected element data tab of data display tab panel 19 Search Results Format Peaks that match the search conditions are associated with both the basic and the shifted sample These peaks are displayed in the search results the order of the displayed data is 1 basic sample 2 associated informati
7. the template to any location as a tab delineated text file We recommend that you do not delete columns not used in analysis at this stage but wait until after the search is finished The data preparation is now complete lt Memory Setup and Startup gt In this section the memory set up and startup procedures are described Memory Setup A large amount of memory is used if a large quantity of data is processed You can set the memory size in accordance with the PC environment n the initial setup the maximum memory is set to 1 GB Xmx1G 1 mn a text editor open launch bat located in the installation folder 2 Overwrite the maximum memory size set in the Xmx option and save launch bat Notepad File Edit Format View Help java ce alibek libs lib 11b Acoxml libk 1 tky Main Pause Starting Up ShiftedIonsFinder for a Windows User 1 Double click launch bat in the installation folder After the splash screen is shown the main frame is displayed Starting Up ShiftedlonsFinder for a Macintosh User 1 Double click launch command in the installation folder After the splash screen is shown the main frame is displayed it doesn t work when you double click launch command 1 Open the terminal Application gt Utilities gt terminal 2 Enter chmod x launch command and perform it 3 Double click launch command in the installation folder After the splash screen is
8. 0133275 0 0000814 5 389642 546 7271 546 7198 7014203 Acuale 58 5 403321 376 8065 375 7993 5502325 Adua 0 0 0 0212050 0 0000153 5382116 1768055 3757993 2141073 6403967 626 6024 625 6851 8052452 Adua 0 0 0 0162649 0 0000101 5 387702 628 6924 625 6851 7768350 y 5404360 5427309 5617237 1933444 yes 0 0 0 0164128 000008544 87347 5427310 541 7237 665080 34 Arusi 74 5 404453 6286904 627 6831 4200300 0 0 0 0158617 0 5 6286903 627 68308 8 Was 75 5 404456 450 7507 457 7525 197026 7 Actual 0 0 9 017278 00000310 0 5 307177 450 7697 457 7624 73539 25 Actual 76 3730011 159455 8 Adua 0 0 00195082 0 3743084 373 8011 60115 07 c l 5405089 544 7291 5437210 91483 19 fAclual 0 0 0 0170049 0 0000362 0070126685 5 388084 544 7290 5437217 3259859 Actual e n 5405099 796 6134 7956061 34235 68 3 0 00150307 0 0000041 5 5 390009 796 6134 795 6061 7928434 5 406607 710 6537 709 6464 6227840 Actua 4 0 00194061 0 0000593 008344498 46 5 387201 710 6538 709 6485 1827952 a 5406543 794 6153 7836080 4349786 Adus _ 15 0 00187302 00000163 0020513 5387013 7946153 7926000 12196 65 82 5 406558 4527000 401 7587 12440 04 Adua c 00173810 00000732 0 1261793864 5 389277 4027050 401 7587 5330 7197 Actuale
9. 183884 148 1162 147 1089 23520 45 5 185717 147 1128 129 0790 390585 9 5 187665 130 0863 129 0790 37127 95 5 193313 289 1618 288 1545 3582 513 5 234062 295 1498 294 1426 4822 191 5 240654 309 1655 308 1583 51311 33 5 241616 310 1689 309 1616 4371 371 5 251558 146 0812 145 0739 23205 06 5 312194 166 0697 165 0625 5 313463 164 0740 163 0667 164 0700 hb Om WN BW et Ow Oods A File Tool Help 5 148228 152 9975 151 9902 724 1895 5 158530 132 0036 130 9963 22403 65 5 173913 179 0703 178 0630 18613 77 5 185799 153 1329 135 0990 287067 5 5 186463 136 1064 135 0991 22461 09 5 187222 152 1296 151 1223 55886 37 5 212068 163 1328 162 12562 8893 542 5 240314 321 2058 320 1985 5143 9638 5 262686 136 0943 135 0870 5944 791 5 3108137 169 0907 168 0835 40845 75 5 311773 170 0941 169 03868 256975 3 5 312288 172 0899 171 0826 10617 23 5 312499 106 0684 105 0611 43289 72 5 338829 258 8994 189 9047 10540 83 The shifted sample information tab 13 lt Management of Element Data gt The element data can be customized as needed In this section we describe how element data are edited added and deleted Editing Element Data Element data information is manage
10. 5 5 187222 152 1296 151 1223 58596 37 tual 6 yes c z 6 6186717 147 1128 128 0790 330665 8 yes 1 5 00015069 0 0000114 007493619 6 167222 152 1296 1511223 665896 37 Acual yes 13 5 312194 166 0697 165 0825 8075626 Acual 0 2 08651026 00004343 2558394248 198 6177298 1680769 167 0696 3945827 4 13 5 312194 166 0697 165 0525 8075 526 Actual 0 3 08683140 0 0003992 2 36101468 199 6 180508 169 0802 168 0729 3940082 Acuale yes 5313463 164 0740 163 0667 2343040 Achar yes 4 0053225 p 53108137 1690907 168 0835 40845 75 Actuals 15 5313358 1650773 1640700 11685 56 Acual 1 4 0 0030452 0 0000141 0083387289 5 3108137 1690907 168 0836 40845 75 jadual 15 5 313358 165 0773 164 0700 11685 56 1 00020854 0 0000062 004820010 5311773 1700941 769 0868 2569753 Actuals yes 16 8921 10690 96 Adua 0 0 00042289 00000201 00776363 5 2588094 1899007 10540 82 Actuals 17 5 352551 140 0108 139 0036 48046 004 0 4 00050791 00000098 0 06804 5 347472 1440243 443 0170 41088 29 Actuale 17 5382584 140 0108 130 0036 48046 004 0 0 0 5296067 00001257 18 5872160 1400107 1300034 3003102 Acuale 19 5357708 1089508 1059433 82625 54 Acual _ 0 0 00062370 00000019 5 351471 106 9506 105 9433 53690 00 Acival 21 5 363757 192 9100 123 9153 13892 05 Actual 0 00058226 00000149 5 357935 132 9101 123 9154 7593910
11. arch results 5 Space where the file names of the selected search results that were processed previously are displayed The files selected here should be prepared as a text file tab delimited format in advance 22 3 4 6 Button for displaying the file selection dialog 7 Button for removing the selected search results from 5 8 Button for joining all selected blue highlight search results 9 Cancel button Click the Browse button to select the basic sample If there is already a basic sample in the box skip this and the next steps The file selection dialog is displayed Select the import data to be used and click the Open button Ft Open La Lo a De li config doc img lib File Name Files of Type Text File tt vl Open Cancel Click the Add button to select the search results that were prepared previously as needed If you do not need these search results skip this and the next steps The file selection dialog is displayed Select the search results to be used and click the Open button reopen m t t l De li config doc li img lib File Name Files of Type Text File bt il Open Cancel 7 After selecting all the files that you want to join click the OK button to start the join process 23 lt Output of Search Results gt In this section we describe how to output search results The
12. can check multiple search results simultaneously Moreover the output file of previous search results and the current search result can be joined In this section we describe how to join the search results Import data Unlabeling Peak1 Shifted sample 13C labeling 15N 180 labeling S4S labeling Output data Unlabeling 13C labeling Unlabeling 15N labelingq Unlabeling 8O labeling Unlabeling 55S labeling Peak1 lag5 1 lag Peak1 Peak1 lag Peak2 lag8 Peak2 lag1 Peak2 Peak2 lag1 Output data JOIN Peak1 lag5 lagO lag1 lagO N 5 1 Peak2 lag8 lag1 lag4 lag1 C8H N10481 Overview of Join function Unlabeling 13C labeling 15N labeling 180 labeling S labeling 21 1 From the Tool menu select Join Files File Stee Help 2 join dialog Join 15 displayed 12C unlabeled Medicago Leaf td Result Data List C 13C labeled_Medicago_Leaf ttt R Join Ea Basic Sampe Select File BB e Browse Result Data List 3 Reset 0 j Cancel 1 Box in which the common basic sample name used for joining is displayed If the basic sample has already been imported for search this name is displayed 2 Button for displaying the file selection dialog 3 Space where the file names of the search result are displayed If the search is not performed no file name 1s displayed 4 Button for resetting the selected se
13. d in a file called atom txt in the config folder in the installation folder Although you can edit atom txt directly you can also edit it by using Element Manager 1 From the File menu select Element Manager AES Tool Help File Import File Export Element Manager 2 The element data management dialog Element Manager is displayed 3 1 0033554 4 4 9957951111 09970347926 S 2 004246177 t OK 8 cancel 1 Column that displays the element names of the element data 2 Column that displays the mass differences of the element data 3 Button for adding element data 4 Button for deleting element data 5 Button for confirming and saving edited contents 6 Cancel button 3 To edit a cell of the element data double click it pk Element Manager Element miz Dif CF 1 9957951111 0 9970347926 2 004246177 OK Cancel 14 4 After editing press the Enter key on the keyboard to confirm and click the OK button to save the edited contents Please note that if the same element name already exists the edited contents will not be accepted Adding Element Data 1 From the File menu select Element Manager 2 The element data management dialog Element Manager is displayed Click the Add button to display the dialog for adding new element data Add Element Data Add Element Data m Bement 100 miz Dif Cance
14. e search results can be output in Excel or text file format the user can perform further analysis or edit the list as needed The tool 15 compatible with the output file of the LC MS analytical tool for metabolomics PowerGet which is available at KOMICS http www kazusa or jp komics Since it prepares text files that follow a prescribed format it also supports analyzed data produced by other software programs Therefore the user can perform a peak search using this software alone after performing peak picking peak alignment and database searching using other types of software Furthermore because the search is basically performed using only accurate mass values the tool is also compatible with analysis data produced using other chromatography mass spectrometers and thus its use is not limited only to LC MS The tool was previously called Metaboloblast but was renamed ShiftedlonsFinder upon general publication Contents lt Search System OVverview gt cccccccccccscecssossssvesssssssesccccscesenecccesssesssesessescececcaseecsccsssssessssssstccceessatees 5 Searcik Erocess add 5 0 10 7 7 Installing Shifted TomsFinderr 7 Uninstalling ShiftedlonsFinder 7 lt Preparing Import Data Used in Search 8 When Using 1
15. ent data multiple m z Dif and RT Dif When you want to use multi element data for the search click the Add button to increase the selection menu for setting the element data and the multiple Setting the Element Data Select any element from the Element selection menu on the search conditions setup panel C is set as the default Shifted Sample 13C laheled Medicaqu Leaf idi LA Sam E T Setting the Max Fold In the search conditions setup panel enter any value in the Max Fold box Integer values from zero to the value set as the multiple are used in calculating Masspy in the direction of addition It is set to 5 by default but an appropriate value must be entered depending on the selected element assuming that the number of that element can be incorporated We recommend that you use a certain degree of margin when setting a numeric value After editing press the Enter key on the keyboard to confirm and save the edited contents Shifted Sample 13C labeled Hedicaqu Leaf ti Element Max Fold ae Setting the m z Dif In the search conditions setup panel enter any value in the m z Dif box It is set to 0 005 unit by default but an appropriate value must be entered depending on analysis conditions such as the performance of the mass spectrometer Additionally the units unit or ppm can be changed by clicking the
16. f txt r Shifted Sample 2 13C labeled Medicago Leaf Element Max Fold 5 6 Add Remove c 0 4 x x s r m z Dif RT Dif 1 Space where the file name of the basic sample that was input 1s displayed 2 Space where the file name of the shifted sample that was input is displayed 3 Selection menu for setting element data 4 Box in which the value of multiple is entered 5 Button for adding 3 and 4 6 Button for deleting 3 and 4 7 Box in which the value of m z Dif is entered 8 Box in which the value of RT Dif is entered 9 Button for starting search 1 and 2 are not displayed before input Details are described in a separate section Configuration of Data Display Tab Panel 1 2 Basic 12C unlabeled Leaf td Shifted 13C labeled_Medicago_Leaf txt d PT ava mac iva mac Sva Intan Praf lani MQA 70 1913 3 ImportData result C 1 Tab that displays basic sample information that was input 2 Tab that displays the shifted sample information that was input 3 Tab that displays the shifted sample data that was input 4 Tab that displays the search results data Details are described in a separate section 11 lt Import Data Input gt In this section we describe how to input import data Import Data Input 1 2 From the File menu select File Import JES T
17. l 4 Enter the data to be added and click the OK button to update the Element Manager table information Please note that if the same element name already exists the edited contents will not be accepted MR Add Element Data Element Manager Element m z Dif 1 0033554 0 9970347926 2 004246177 Glucose 162 0528234 Element Glucose miz Dif 1 62 0528234 OK Cancel OK Cancel 5 Click the OK button in the Element Manager dialog to confirm and save the edited contents 15 Deleting Element Data 1 From the File menu select Element Manager 2 The element data management dialog Element Manager is displayed 3 Select the item to be deleted and click the Delete button ya Element Manager Element miz Dif 1 0033554 5 1 9957951111 N 0 9970347926 2 004246177 Glucose 182 0528234 4 A dialog to confirm deletion is displayed Delete Data Glucose 162 0528234 Yes 5 Click the Yes button to update the Element Manager table information ys Element Manager F r Element m z Dif 1 0033554 1 9957951111 0 9970347926 2 004246177 Add 2 00 OK Cancel 6 Click the OK button in the Element Manager dialog to confirm and save the edited contents 16 lt Search Conditions Setup gt In this section we describe how to set the values of the elem
18. lt Basic sample peak list Associated information Shifted sample peak list Ave R T Ave mass Lag RT m z Difference Ave R T Ave mass min detected 1 times Difference u ppm min detected n b Mun sn sn Mont M n s 109 Tan M sn sn Overview of the search process flow lt Setup gt In this section the operating environment and methods for installing and uninstalling this application software are described Operating Environment The application software was developed using the Java programming language The Java Runtime Environment JRE 1s required to run a Java program The JRE must be installed in PC environments where it has not already been installed or where an earlier version than JRE version 1 6 0_10 set forth in this specification is installed The recommended environment is as follows OS Windows XP or above MacOS X ver 10 9 was used for an operation check CPU Intel Core 2 Duo equivalent or above Memory 512 MB or above depending on processed files Java JRE Version 1 6 0_10 or above Installing ShiftedIonsFinder The application software is installed by decompressing the downloaded compressed file and locating the installation folder called ShiftedlonsFinder on a local drive any location The installation folder contains the following folders config This is a folder for storing basic information A file called atom txt editable by Element Ma
19. nager which contains the element data used in the search is saved in this folder doc This is a folder for storing the manual and the templates used in the creation of import data and created import data However created import data do not necessarily have to be saved in this folder but can be saved in any location img Images such as the ShiftedlonsFinder logo are stored in this folder lib Programs required for startup are stored in this folder launch bat Starts up ShiftedlonsFinder for a Windows user when double clicked launch command Starts up ShiftedlonsFinder for a Macintosh user when double clicked Uninstalling ShiftedIonsFinder The application software is uninstalled by deleting the installation folder that was located on a local drive any location lt Preparing Import Data Used in Search gt In this section the preparation of data for use in this application software is described The import data used in the search function in this application software must be prepared as a text file tab delimited format Further the values of Ave mass detected and Ave R T min must be prepared as items used in computation where Ave mass detected is the m z value of the detected ions and Ave R T min is the retention time The names of these columns must not be changed because calculations in this application software are performed based on their recognition In analyses such as in fusion analysis an arbitrar
20. on and 3 shifted sample from left to right Associated information is as follows Lag times Value of multiple of the search hit RT Difference Difference in elution time of the peak of the basic sample and the peak of the shifted sample Units are minutes min m z Difference u Difference in the m z value of the peak of the shifted sample and MasSpyp Units are unified atomic mass units u m z Difference ppm Difference in the m z value of the peak of the shifted sample and Masspyp Units are ppm File Toot Help p Basic Sample Basic 12C untaneled Medicago Leaf tit 1 planaied_Mecieags esi 2 3 120 unlabeted_Medicago_Leat tt No ave RT i Ave mas Aw mas Ave imen Pretioniz_ Ave MSM 2 BC Lagi RTO flere miz Dftier myzOifer ave eve mas Ae mas Ave intan Prefioniz_ Ave WSM Shifted Semple 2 5 156407 1829851 181 9778 3017330 Q 4 0 4434386 0 0000106 0 92 82 5 599845 1829851 181 9778 20583 35 Actual a 13C a9piod_Medicago_ Leali 3 5 150229 190 0294 198 0221 1481303 Acua 0 0 04308520 0 0000204 0 102497 5 590081 1990294 108 0221 8585510 javais 1 5 5 463854 146 1152 147 1089 2352045 Actuals 0 5 00019145 00000564 0 3535307383 5 185799 153 1329 135 0990 2870575 iclu lv ves Element i Fold Add Remove 5 183384 148 1152 147 10893 23520 45 Actual 4 0 0033384 00000007 000450138
21. on dialog is displayed After selecting the folder name click the Save button to output the search results file The output information is recorded as text files in the folder Look 2 4 ii config l img lib 19 launch bat File Name Files of Type 25 lt Terms of Use gt 1 This application software will be used for research purposes only It 1s available for commercial use at a cost to be negotiated with Kazusa DNA Research Institute referred to as the Institute hereinafter on a case by case basis Partial rights may be requested 2 This application software will be used only by the laboratory of the requester and will not be transferred to a third party 3 Modifying translating reverse engineering reverse compiling or reverse assembling this application software is prohibited 4 When publishing research results obtained by using this application software it will be clearly noted that the application software provided by this Institute was used 5 This application software is provided free of charge and the Institute makes no guarantees regarding its performance Furthermore the Institute is not in any way responsible for damages incurred due to either the use of or the inability to use this application software 26
22. ool Help File Import File Export Element Manager The file import dialog File Import is displayed r Basic Sample 1 raaa Select File man r Shifted Sample AC pees 6 Select File Browse Pok cancer 1 Box in which the import data file name is displayed 2 Button for displaying the file selection dialog 3 Button for confirming input of the selected import data 4 Cancel button Click the Browse button The file selection dialog is displayed Select the import data to be used and click the Open button If you want to import multiple shifted samples please select all shifted samples to analyze 12C unlabeled Medicago Leaf ixt iki 13C labeled Medicago Leaf ti File Name 13C unlaheled Leaf fixi Files of Type Text File bd 12 5 When the import data has been selected the file name of the selected import data file is displayed in the File Import dialog 6 Click the OK button to complete the input of the import file The basic sample and shifted sample data that were imported are respectively displayed on the basic sample information tab and shifted sample information tab 1 File Tool Help 5 104595 124 5839 123 5766 11964 07 5 153748 129 5761 128 5688 14246 18 5 156407 182 9851 181 9778 30174 30 5 159229 199 0294 198 0221 14813 03 5 181392 133 0972 132 0399 30963 87 5
23. output file is in Excel format x sx or text format txt Output information 15 as follows SettingData The name of import data and search conditions BasicSample The peak list of import data for BasicSample No _ImportData The peak list of import data for ShiftedSample No _result_ Element The Search results el The number of imported files 57 The name of selected Elements Output as Excel Format 1 From the File menu select Export JES Tool Help File Import File Export Element Manager Exit 2 dialog to select export file type is displayed Select Excel File and click the OK button bed File Export Select File Type Excel File _ Text File OK Cancel 3 The file selection dialog is displayed After entering the output file name click the Save button to output the search results file The output information is recorded in each tab in an Excel file Save Lookin 1 1 5 2 gt da D Bi config ii doc li img liv launch bat File Name Files of Type COo imi Save Cancel 24 Output as Text Format 1 From the File menu select Export Tool Help File Import File Export Element Manager A dialog to select export file type is displayed Select Text File and click the OK button Select Fil C Excel File Text File ox The file selecti
24. rch Results s sssss isi iiii l 19 Search Execution Method ALA A 19 Search Results Format Hise sci ice caveats sects a A d a a a das 20 lt Join the search result DL de i leet rar htt Aa 21 zOutputotcorelhi CSU SS b b basabasda 24 a OUtput as Excel Format a A Output as Text Format R A a DR E Ro s c Terms of Use lt Search System Overview gt In this section the process flow according to which this application software searches for peaks that have specified mass differences is described The data that are the object of comparison are called the import data and are called basic samples or shifted samples depending on the respective application Furthermore the data that describe the specified mass difference are called element data The three parameters that are set and used in the search are the multiple Max Fold the mass to charge ratio m z difference threshold m z Dif and the retention time difference threshold RT Dif For example when searching for peaks labeled with a stable isotope the unlabeled sample is the basic sample the sample externally labeled with a stable isotope is the shifted sample and the mass difference between the principal isotope and the stable isotope used in labeling is the element data The multiple is the estimated maximum number of stable isotope atoms incorporated in
25. shown the main frame is displayed 8 O00 ft seimeiken bash 80x24 a Last login Fri Jun 27 18 28 08 on ttys000 E seimei ken no Mac Pro seimeiken chmod x Launch command lt Screen Configuration gt In this section the screen configuration is described Configuration of Main Frame shiftedtonsFinder Sas File Tool Help m z Dif RT Dif 0 005 unit ppm 0 3 START 1 Menu bar This is the menu for file management and other tasks 2 Search conditions setup panel This is the panel where search conditions are set 3 Data display tab panel This is the tab panel where import data and search results are displayed Configuration of Menu Bar File Import Menu for importing import data used in the search Details are described in a separate section Export Menu for writing search results Details are described in a separate section Element Manager Menu for managing element data used in the search Details are described in a separate section Exit Menu for quitting ShiftedlonsFinder Tool Join Files Menu for joining multiple search results Details are described in a separate section Help Open Manual Menu for displaying manual of ShiftedlonsFinder About Menu for displaying version information of ShiftedlonsFinder 10 Configuration of Search Conditions Setup Panel r Basic Sample 1 12C unlabeled Medicago Lea
26. the compound and the m z Dif and RT Dif are the allowable limits of error Search Process Flow 1 hypothetical m z value Masshyp is calculated by adding the m z value of the selected element data to the m z value of ions present in the basic sample Masspyp is calculated for each respective value from zero to the value set by the multiple Max Fold F 2 A search is performed to determine whether the calculated Masspy is present in the shifted sample M Filters are applied using the m z Dif m or m and RT Dif t values that were set 4 The search results are displayed Basic sample peak list Element data Parameter Ave R T Ave mass Specified mass difference Max Fold F min detected 13 1 0033554 m z Dif m u or m ppm 15N 0 9970348 RT Dif t M 180 2 0042462 b2 34S 1 9957951 Step2 Peak search Shifted sample peak list Ave R T Ave mass VVhether min detected M s1 s1 Tot 1 0033554 x 0 Mp1 Ton Mp4 1 0033554 x 1 1 0033554 b1 1 0033554 x F 1 0033554 x F Mp1 F T Mya 1 0033554 x 0 1M Step3 Filtering IM m z Dif m m Mu Mon X 106 Mpn m z Dif m Teni s RT Dif t T T l 1 T Mpy 1 0033554 x F 1 Monit 1 0033554 x F Moy et 1 1 l I 1 Lo Step4 Display of search resu
27. y numeric value must be entered for Ave R T min even when there is no retention time As a precaution please make sure that the two import data to be compared are in the same format Details for preparing data when either PowerGet or other programs are used are given separately below When Using PowerGet Please refer to the PowerGet manual for details on using PowerGet An example of outputting data from PowerGet is described below as well as a precautionary note 1 From the File menu select Output and on the List tab check all boxes in Alignment and Samples 2 Select Each Sample from Group by and click the Save As button to output the file 3 Open the output file in Excel and save it as a tab delineated text file to any location We recommend that you do not delete columns not used in the analysis at this stage but wait until after the search is finished The data preparation is now complete Note The name or order of the columns on PowerGet is sometimes changed with upgrade When Not Using PowerGet As described above the Ave mass detected and Ave R T min columns are required A recommended template is provided in the form of an Excel file in the data folder It 1s recommended that you use this template when performing this operation for the first time 1 Open the recommended template file in the data folder 2 Enter values in the corresponding columns of the template 3 Output
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