ShiftedIonsFinder (Version 1.1) User`s Manual
Contents
1. sees 6 Preparing Import Data Used in Search sse eene eene 7 When Using PowerGet sse nennen eee ee nennen nnne nenne nenne eene nenne nennen nennen J When Not Using PowerGet sse eene ne nennen eene eene 7 Memory setup amd Starp aisina na a a muet emu equ equo dog uo uana NENE 8 Memory SCOP Cr X 8 Starting Up ShiftedIonsFinder ccccccscssssscscscesecssscesecccececseeescseseccccseccececseccecseecececeeees 8 screen C onfigurationl ure ce et rni ae ade Ca ae cade tee ae eR ade esed tue deoa ade asks 9 Configuration of Main Frame essen n eene eene esses sse se saa arre nere eee s 9 Configuration of Menu Bar 00 00 0000 ccccccsssssssssseeeccccceeeeeeeccaaaassssseseeeececeeeeeeeeeessauaassesseeeeeeeeeeees 9 Configuration of Data Display Tab Panel sssssssssseeeee 10 Import Data Input oerte ted tes too hdd tette d ieiunii ieciee iden adim be enu 11 hmport Data TMU Sariei O e ENOO 11 Management of Element Datad ccccccccccccccccsssseeeesseeeececcceeeeeeeecsaaaasseseeeeeeeeeeeeeeeeeeaaaas 13 Editing Element Data ccccccccccssseeenosnsseveessssssccccccssesececccssssssssssssssccccsscsteeceesssssesssssessecs 13 Adding Element Data 0 0 0 0 ccccccssssssssssssseccccceeeeeeeeaaaaaaassessseeeeceeceeeseeeesaaaaaaesasseeeeee2. The Join function combines into a table the multiple search results in which the same basic sample is used Thus you 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 Shifted sample SC labeling Output data Unlabeling C labeling Unlabeling N labeling Peak1 lag5 Peak2 lag8 Output data JOIN Peak1 Peak Peak2 lag4 Peak8 Peak2 lag Unlabeling 5C abeling 5N labeling O labeling S labeling C5H 01 Peak1 lag5 P Peak2 lag8 C8H N104S1 Overview of Join function 20 l From the Tool menu select Join Files File BERE Help Medicago_Leaf tt Result Data List C 13C labeled Medicago Leaf txt l ad Join m Basic Sampe a Select File RN g Prowse Result Data List 3 4 Reset Bok C cancer 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 is displayed 4 Button for resetting the selected search results 5 Space where the file names of the sel
3. Please note that if the same element name already exists the edited contents will not be accepted V Add Element Data ese FQ Element Manager Element Glucose Element m z Dif C 1 0033554 S 1 9957951111 N 0 9970347926 O 2 004246177 OK Cancel Glucose 162 0528234 Fox cancer 5 Click the OK button in the Element Manager dialog to confirm and save the edited contents 14 Deleting Element Data l From the File menu select Element Manager The element data management dialog Element Manager is displayed Select the item to be deleted and click the Delete button 1 995 951111 0 9970347926 2 004246177 Glucose 162 0578234 A dialog to confirm deletion 1s displayed Delete Data Glucose 162 0528234 VR Element Manager mx Element m z Dif Add 1 0033554 1 9957951111 0 9970347926 2 004246177 ozono OK 6 Click the OK button in the Element Manager dialog to confirm and save the edited contents 15 Search Conditions Setup In this section we describe how to set the values of the element 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
4. as the default Shifted Sample 13C abeled Medicago Leaf txt Element Max Fold Add Remove BE et E v 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 Massy 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 abeled Medicago Leaf txt Element MaxFold n a 00 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 unit or ppm button m z Dif 0 005 unit ppm 16 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 c
5. menu select Export Tool Help File Import File Export Element Manager 2 The file dialog is displayed Lookin jj 1 152 x Bj config mi doc img Bj lib launch bat File Name Files of Type 3 After entering the output file name click the Save button to output the search results file 23 Terms of Use 1 This application software will be used for research purposes only It is 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 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 4 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 24
6. s v r m z Dif RTD uL 8 P START 0 005 unit ppm 0 3 START 1 Space where the file name of the basic sample that was input is 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 unlabaeled Medicago Leaftxt Shifted 13C labeled Medicago Leaf txt hulls dun EDT S due mac hua mac fue Intan Draf lani duo MCI dei de SIE n h 3 4 3 ImportData result C 1 Tab that displays the 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 10 Import Data Input In this section we describe how to input import data Import Data Input 1 From the File menu select File Import EI Tool Help File Import File Export Element Ma
7. 0 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 E 164 0700 NS hb Om WN BW et Ow 0000 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 968 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 12 Management of Element Data 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 managed in a file called atom txt in the config folder in the installation folder Although you can edit atom txt directly you can also
8. E 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 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 ShiftedIonsFinder 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 Manager 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 ShiftedIonsFinder logo are stored in this folder lib Programs required for startup are stored in this folder launch bat Starts up ShiftedlonsFinder when double clicked Uninstalling ShiftedIonsFinder The application software is uninstalled by deleting the installation folder that was located on a local drive any location Preparing Import Da
9. ShiftedIonsFinder Version 1 1 User s Manual Introduction 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 the searc
10. ected search results that were processed previously are displayed he files selected here should be prepared as a text file tab delimited format in advance 21 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 3 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 4 The file selection dialog is displayed Select the import data to be used and click the Open button V4 open on 6 ar De Bj config 8j doc ij img B lib File Name Files of Type Text File tt iv Open Cancel 5 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 6 The file selection dialog is displayed Select the search results to be used and click the Open button WX Open Ex a 6 a De Bj config doc ij imo Bj lib File Name Files of Type Text File bt vj Open Cancel 7 After selecting all the files that you want to join click the OK button to start the join process 22 Output of Search Results In this section we describe how to output search results The output file is in Excel format xlsx 1 From the File
11. edit it by using Element Manager 1 From the File menu select Element Manager AES lool Help File Import File Export Element Manager 2 The element data management dialog Element Manager is displayed JN Element Manager W 2 E ement i 1 0033554 4 19957951111 P Delete 0 9970347926 2 004246177 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 bs Element Manager Element miz Dif 1 9957951111 0 9970347926 2 004246177 OK Cancel 13 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 3 Click the Add button to display the dialog for adding new element data Add Element Data be Add Element Data m m cement I m z Dif OK Cancel 4 Enter the data to be added and click the OK button to update the Element Manager table information
12. eeeees 14 Deleuns Element Data 5 uoce RII cc 15 Search Conditions Setup ccc cccsssssssssseeeeccccceeeeeecaaeaaesssseeeeeeeecceeeeeeeeesaaaaaaseseeeeeeeeeeeeeeeeeeaaas 16 Setting the Element Data 0 0 cccccccccccssssssseseessesseseeseeseeeeseeeeeeseeeeeeeeeseeeeeeseseeeeeeseeeeeeeeeseeeees 16 ssset ne the Max Eold saisie etal bap tat ite DM P late bhatt eal bhai 16 mC NN the m 7 DIE ud ih ete ida ele ep sts a lion sich na ie uote aisha ete asus ais 16 Settna the RT DI gles ae a cancers es erro rette rustica stones tones ueu 17 Search Execution and Search Results Format gt cccccscccscccceccceeeeesesseeesesssnneeeeeeeeeeeeeees 18 Search Execution Method eoo t bti Hed ra recens olt se eal adus ea Uta cha UM dotate 18 CATCH Results Format RUSSE T E E cadena E E 19 Jom the search result gt 0oeooooeoeeeeeeeeeesesssssssssssserrereeessssssssssssserrrreeeeeessssssssssssserreeeeeeesssssssssseeo 20 Output of Search Results ssssssssssss II III III In nnn nn n nnne nnn n nnns s sns r enis 23 lt lerms OF SOP c aeccheeieade 24 Search System Overview In this section the process flow according to which this application software searches for peaks that have specified mass differences 1s 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 re
13. h results can be output in Excel or text file format the user can perform further analysis or edit the list as needed The tool is 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 ShiftedIonsFinder upon general publication Contents Search System Overview gt ccccccccccsssesssssssessssessvecccccscseeecccnssseessesceseccccceasteecccesssessssssssssccessaesees 4 Search Process FLOW A 4 cho 6 Operating Environment ooo e ep rra eden elo ret et dela s re soe OL UR iE dba c do nue 6 Installing ShiftedIonsFinder ccc ccc cccccccssscccccccccceeeeccccassesessseeeeecececeeseeesessaaaaaasseeeeeeeeeeees 6 Uninstalling ShiftedIomsFinder
14. ha T 31 xum 1ETERO PNIA p 1 5 19 L TNE PETRI H facials Ti eT BS 4255858 Bibi piae Li 7 Seri Gl et Tes pu 71 441530 SAIPRO SAJEN OHA ja 0 4g i EG 3 ee T4 BEHI EE et M o n a 5 i ENER UJA ee a m Aus eae Pa B a EL xn ume o ail Mwca HAN pictus s 7 he Bake FUTO ei Duk Fah PMi bigg fee T LASIS KLATI Silpa PMII peia A n wA HEGI AL MT WEM piia m fees o TOREM Ti DEST Bere Que i n a Tei Pied ii fe a LAELUT TUL TIAR NT D a D x Wi FE UDIN T t ET TH PRRSUCEO didi 35 LD cuR aE p t Bii NMG Tiimin tes uait i Iati Bare AR Tibi toa 1 33 iTe ait T dT Gg eeu H JAM LST TA TEMA idea as B fn TET STS TORE factual o Argis TIa TUL AS Sea d a 6 v Emu 3 5445 1i 734 rl LI 3er ITA 0 SS Rhea 1 n Egia Amy JM HEMA peiie m 4T7 8 AGS MOTTE 1 E fer WEET PEOR S 003844 fiie qu Scb Wee CIRCE AP pee 1 5 Il Sa pe uh cioe Wee mp Eu LL i teach path oko ina 1 E Chr ELT Ce te quide q amp D amp R phd pii sa om p LEVAT ism ptas nenas 6 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 19 Join the search result
15. idi diiit dei pas a EET GOMDEHSON ER EME poi Q h SB A 325403 ee feta i ikia See LT a iiig ian kien ETT a 22397328 TRI TRR WX So Q L 18 er TH MEAT ENI zi SPA Dalit GIBATER iiia ai A Ae GME 228474 lacia E Ayer ZITAT ae BL Dea E b 1 EAHIL SMETU Sar HMH zs zm a YER J THT dea Ya EH IER lc SyaT AT NET 733b dao ke D Saw LN Te OE pe oT fs Mis Jih 103d EE a B Mo gx Hai f peu J a TO TRA BET ppm g b m L A Tio PIa F parua z SI VM 1150085 HTMs m1 1 5 X31 LEIA Ho z5431 piia ce gai 524 TATS 5237498 fs ple 1 z Smam L eee jin ut EHHA GT SRT RTL ete D 1 COM HATTE TF jiii X Ax Mam aa 355 443 4e 4 LJ Lx LM ARMS Te jc 1 Hew Wao DORODTT iania ST c eo Jaroa TDAI jauni LES 23978978 TE MT Gh Pa pum a 5 E CHIHI AVE Wart l pe my ATTO AE ITE a B T o VMA i MAn piae pes ET IANA i042 325 amp 84078 qu331 01 ficka s Bn 14 al ST tein fe nh 087 mipik Ia THN As B aa S04 Bil gua 4 facts n inm edd THEY pomme ps oo T 43 BH pero Se 5n aedium 2 ee a pk ma a B H 3058 HARA 2008742 Me Pume pii m ie Se ga IERI Ta L i Gh See HIPT Ma Decius ar BONS 2015637 Se NE head a Li SRN SLC 22000415 20390822 Aue ig ma See Thee T4153 Au B fu ii MATE peuss y Kt mamisgT FEIRAL SH pia e prz m LE i A SA 23128080 FMA jiria A mami Jabra DONEN T 1 25 14 a Q eT Jappen Tac phus Lo densa SA Jn WH Bate s a Nu SoS EST SST To o c
16. k 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 Massy Units are ppm nuE Fu cp HAE rac ipli 9 msi toC nisle t Meir Lear e LEE 2 3 AUC urniasdin DORE E ji gt ro us tuas maim Ji AB TI amma EDGE MATS Peces je Dx RC nne ee fee meter Bone Ad ema meras e mem Pea ve MEN Safni Templa So Wei Wee GQP43I oko p pp WRL MUNE meskes ack P Tiaabeweg edax Leer ba 1 5108229 WL OES ane Me a EE asuma EB pt n Dern Max old r 5 Pts las d iF ia CER ZUR al ihm E bens ie i LEUT PENI i p O aao anaa 5 Iiki nii Fia HADAL iiai e 4 ae ows 1 eh lh jak L 3 T TL a L RAM OF AREE paii qua 4 E E Starter 1995 AN ESO Pa aha pi 3 1351162 ibadi 1840824 pe a gt Sueded ae ifs uBdE e TS wpT R maagia ChctRI jani 13 iym quif g Jiag IPSOS Aeg a j n a iiss inel qug Hee fac t 5383451 1040749 MAME 2240080 e qe 4 5 LI HOD GORDWU OT picks jara ibi BLO PRE phia 1 D S303 o qTNDES TRO ipsm ya j ki 1 ynas RAO ME TESE ncs 1 1 D io 2513751 T w aS 44 STESSO WOH Dum 13 ASS Td ET hea rius mi jariji 1385038 Lae Jai E hata eh 4160175 eS ft rea eps 1380004 eee ioca a b ET LI w
17. llation folder After the splash screen is shown the main frame is displayed Screen Configuration In this section the screen configuration is described Configuration of Main Frame WX shiftedIonsFinder File Tool Help PD Basic Sample Shifted Sample miz Dif 0 005 unit ppm 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 ShiftedIonsFinder Tool Join Files Menu for joining multiple search results Details are described in a separate section Help Open Manual Menu for displaying manual of ShiftedIonsFinder About Menu for displaying version information of ShiftedIonsFinder Configuration of Search Conditions Setup Panel Basic Sample 1 12C unlabeled Medicago Leaf bt Shifted Sample 2 13C labeled_Medicago_Leaf ttt Element Max Fold 5 6 we Add Remove Ic 3 4 n ada Remove
18. nager r Shifted Sample 1r i P T P Select File isana Wok Cancel 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 4 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 txt 5 13C abeled Medicago Leaf txt File Nama 12C unlabeled Medicaga Leaf txt Files of Type Text File txt M 11 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 A 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 183884 148 1162 147 1089 23520 45 5 185717 147 1128 129 0790 390585 9 5 187665 130 0863 129 079
19. onditions RT Dif 17 Search Execution and Search Results Format In this section we describe how the search 1s 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 bt Shifted Shoot 13C labeling 33 01 When the process is finished the search results are displayed on the Output tab of the data display tab panel The flow of the search including setup and related functions performed up to this point 1s shown below Importing of import data Selection of element data n Setting Max Fold i Setting m z Dif i Setting RT Dif i Start of search by clicking the Start button Display of search results data on result the name of selected element data tab of data display tab panel 18 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 information 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 pea
20. spective 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 the compound and the m z Dif and RT Dif are the allowable limits of error Search Process Flow 1 The hypothetical m z value Masspyp Mon 1s calculated by adding the m z value of the selected element data to the m z value of ions My 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 SC 1 0033554 m
21. ta Used in Search 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 arbitrary 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 dele
22. te columns not used in the analysis at this stage but wait until after the search is finished The data preparation is now complete 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 is 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 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 Memory Setup and Startup 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 In the initial setup the maximum memory is set to 1 GB Xmx1G l Inatext 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 cp ilib Xilib lib lib ooxml lib X XmxlG tkv Main palse Starting Up ShiftedIonsFinder 1 Double click launch bat in the insta
23. z Dif m u or m ppm te M 15N 0 9970348 RT Dif t T M 180 2 0042462 b2 b2 34S 1 9957951 Mon ToN Step2 Peak search Step1 The calculation of the hypothetical m z value Shifted sample peak list R T Ave 3 The hypothetical m z value hypothetical peak list Whether Bat detected Ms M M 1 0033554 x 0 M MES M 1 0033554 x 1 M 4 1 0033554 M 4 sN M l l H M 1 0033554 x F M 4 1 0033554 x F My f Step3 Filtering e Mp2 1 0033554 x 0 ziMj My201 nan I ou ET c Ra IM Men d m z Dif m Mp Mi 1 x 10 Ms jd m z Dif m IT Taal a RT Dif 7 t r L I I I l l I I l I I I L oct Mpy 1 0033554 x F My 1 0033554 x F Mew e l cr Step4 Display of search result 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 times Difference u ppm min detected T sn n P n Msn f W Min E Men t Mr x Mey x 10 Mont Most M sn sn Overview of the search process flow Setup 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 is required to run a Java program The JR
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