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1. 7 Run a Standard Tune to use even more parameters 10 to 15 minutes a Click the Instrument State tab b For the Instrument Mode click Extended Dynamic Range optional Mark or clear the Fast Polarity Switching check box d Click Apply e Click the Autotune tab f Mark the polarity polarities to use when tuning under TOF on the Autotune tab g Click Standard Tune h Click Start Autotune If results are acceptable continue with step 8 If Standard Tune produces unacceptable results you can do an Initial Tune If this also fails to give acceptable results please contact Agilent Field Support If you want use custom tune parameter values you can also do a Manual Tune 8 Set the Mass Range and the Instrument Mode that you want to use to acquire data a Click the Instrument State tab b Select the appropriate Mass Range c Click the appropriate Instrument Mode d Click Apply Recalibrate if necessary 9 Calibration is done when you click the Check Tune button the Quick Tune button the Standard Tune button and the Initial Tune button If you just completed one of these tasks and if any of the following are true you only need to recalibrate e You change the Instrument Mode in the Instrument State tab e You change the Mass Range in the Instrument State tab e The peak abundances are above approximately 480 000 for the 6550 Q TOF or above approximately 650 000 for other Q TOF and TOF instruments You have to d
2. 22 Prepare the TOF and Q TOF instrument e If you did monitor the LC baseline with the DAD change back to the default TOF or Q TOF displays a Right click the chromatogram plot and click Change b Select the MS signal and click OK View the system logbook for events and errors As you prepare the instrument you may run into an error that you wantt troubleshoot You do this through the System Logbook Viewer e Click the Log icon in the toolbar of the Data Acquisition window and view the logged events e Or right click the icon in the system taskbar First click Enable Notification Then right click the LOG icon and click Configure The system can notify you of new errors and warning by showing messages from the taskbar Set up and run a method An Agilent MassHunter Workstation software method for the Q TOF can contain acquisition parameters qualitative analysis parameters or both In the Data Acquisition method you can specify whether or not to run a Qualitative Analysis method and whether or not to run a Quantitative Analysis automation You specify whether to copy or link the Qualitative Analysis method and the Quantitative Analysis method to the Data Acquisition method When you run multiple samples in a worklist with this m method you can specify whether to run both data acquisition and data analysis or to only run either data acquisition or data analysis If you run a single sample in the Data Acquisition program th
3. Vials 1 We have a set of recommended vials that we can suggest 2 Alternatively look at the sheet taped to the wall and confirm that vials fit the dimension 3 Always use the vial cap Finally if you run into issues let a staff member know and put an instrument down sign up 11 Agilent FTIR iii iv The FTIR instrument is located in MIC 109 Login is with Yale Net ID and password You should create a folder with your name inside the data folder for your samples It is equipped with an ATR with Diamond crystal The ATR has to be cleaned after each measurement Keep in mind the film left over is often more reflective than the samples applied due to better contact which can lead to false spectra If unsure about the quality of the cleaning a new background spectrum should be acquired prior to applying the sample to the crystal The setup should be cleaned using KIMWIPE moistened with iso propyl alcohol Please do not squirt the alcohol directly on the plate The applied pressure has to be adjusted to the quantity and nature of the sample the thicker the sample is the higher pressure should be in order to have better reflectance Generally 20 mg of solid or 50 ul of liquid sample are sufficient The high pressure clamp should be turned to its slip clutch limit to achieve maximum pressure 2 clicks The pressure has to be released in order to be able to remove the clamp If this is not done the pin will hit the diamo
4. 6 20 2000 L3 37 AM 29 9009 9 3 37 AM amp 29 2003 9 L3137 AM 28 2008 6 13 37 AM 6202000 9 13 37 AM 0 23 2009 amp L3 37 AM 28 2005 amp 13 37 AM 10 2 2011 0 13 05 AM 10 2 2011 9 1352 AM 30 10 Anew window will open for with the measurement parameters 11 For kinetic runs choose number of repeats and time intervals per repeat B Wallac Envision Manager 1 11 Instrument connected File Ed Vew Toos Actions Heo o 0 1 JC 8 of x O B Xx Perzerd Up Sart Lakest Run Lack _ Undo Mess cut Copy Duplicate Delete e Roader Coral Tb COCHE aed E Protocols Protocol Generel settings 8 use Protocols i E output settings S O Larthasusen EE Label valid labels marked with ar ES Plate Optimization me Gene aser o fl iawethirtsmeen a a Q FP methods Z Cakdations Optmizations Measurement Repeats Test Lartha FAS Number of plate repeats 1 ee FF stare plate ropes each Ez TbShuta Fkterbium Tb Larkha creen Breasts H Assay exemples H Wallac protocols D nesuts Me deniers A Dispenser Control E Barcode Settings amp Render Settings 4B Recycle Bin 12 When finished select start button at the top of the screen It will take you through the optimization wizard The optimization protocol standardizes the sample height and gain for your specific assay 13 The assay wizard will open automatically Select optimize existing protocol then select Next Se
5. E O Acc eramplar Fred mess rarert height mmi 18 Q Walle protocole Ress d KE nsertey B 1 i i i i i i i i i i i i i i i i i i i i i i t Dispenser Control a Measurement Technolo pss FE aber Nurber of runs 6 Now select Well Selection A new screen will appear with a plate schematic allowing you to use the drop down tool bar to define your wells as needed Controls or Blanks for auto subtraction if you chose Tb LanthaScreen C Pretocel General setti pepiczzezi Next index Fil start FB styler Well sze Sz Bowamee p up wee Hm Hem Optimisation C C3 arenar Meere en fuddirerixee samples by selecting acprape ate option below end damna Een the plate GFP methods au EEEE 4 Cyquart Fluorescence Intenatzy Lu test Test Lantha FAS op SO BB ee Measurement Technologies t ii HE IE A dd p g Ej E Reside Settings H Recede fin eoocccoocoococo000 606669606006 06086 o0000000000000 e660600000000000 GOOO AOG OG ecc0000000000 oeo00000000000 eoc00000000000 B g 1 z 6860905600 SGOG006006 7 Right click on Well Type to reveal several different activities Measurement Kinetics Shaking Temperature Control 29 8 Select Measurement in the protocol window
6. Instructions Occur approx every 2 3 months 1 2 Before Filling please ensure all tools transfer lines gloves etc required are available and the Helium gas has an ample amt to fill at least 500psi Read the tag on the Dewar to ensure the tank was filled recently and the amount ordered was delivered Measure the Helium 1 2 3 4 Open top valve keeping hands and face away from plume Submerge the thumper tube to bottom of tank place marker at that point Slowly left tube feeling for changes in the frequency will get more rapid as the top of the liquid is reached Place marker there and measure the distance in inches to get the liters consulting the flip side Helium Calibration Chart must put the Meter on Fill Mode On 600 Meter hit enter minus enter On 400 s Meter hit the fast rate to go into fill mode Hook up and turn on Helium cylinder w gauge to Dewar to the Vapor Phase Valve 600 NMR Pre fill fill and post fill 1 2 3 4 8 Remove the black clamp at T joint and stuff hole with Kimwipes Remove black cap on fill tube and insert filling apparatus tube leaving covered Put one end in the Dewar handing the other end to the magnet filler Once the Helium starts coming out of tip as liquid immediately take cap off insert line into magnet about 1 2 from bottom remove towel and screw cap to seal On Helium Dewar open the Vapor Phase valve and regulate the flow to
7. Method Editor toolbar or you select one from the list that appears when you click Method Open b Right click an LC module in the Instrument Status window to change any non method control parameters if necessary c Monitor the baseline and adjust the plot to make sure the column is equilibrated and the baseline stable 4 Set up to view real time parameter values actuals As you prepare for a run and during a run you want to see the actual values of the instrument parameters You can do this in the Instrument Status window a Right click the Actuals window to see the Setup command b Click Setup to bring up the list of Actuals available for monitoring If you have configured a TOF instrument the actuals for the TOF instrument are displayed instead c Add all the parameter values you intend to monitor you can customize the color of the background and the text You can also add minimum and maximum values to use if the value is not within the given range then the background of the value is set to red in the Actuals window d Click OK Set up real time plot displays As you condition the column you set up the displays to monitor the effluent e Right click the Chromatogram Plot window and click Change In the Edit Signal Plot dialog box you can select multiple display signals and change the display range Prepare the TOF and Q TOF instrument You need to tune the instrument the first time you use it or after maintenance s
8. Polarity Switching enable Fast Polarity Switching on the Instrument State tab and recalibrate If you have a Q TOF instrument Fast Polarity Switching was disabled before tuning the quadrupole Follow these steps to enable Fast Polarity Switching a Click the Instrument State tab b Select Enabled for the Fast Polarity Switching c Click the appropriate Instrument Mode d Click Apply e Wait 20 minutes for the instrument to equilibrate f Click the TOF Mass Calibration tab g Click the desired polarity in the top left corner of the Tune window h To select a different set of masses click Load or select or clear individual masses in the list on the left side of the Tune window i Click the Calibrate button j If you want to calibrate the TOF analyzer in the opposite polarity repeat step g through step i Tune reports are automatically generated at the end of a tune 21 Calibrate the mass axis During calibration a sample that contains known masses is infused into the source and the actual flight times for ions of known masses are measured These times and exact masses are used to calculate updated calibration coefficients This process ensures accurate mass assignments for unknowns Agilent recommends that you do this regularly Calibration is done when you click the Check Tune button the Quick Tune button the Standard Tune button and the Initial Tune button If you just completed one of these tasks and if any of the followi
9. Segment section and click Add Time Segment The time segment uses those parameter entries with seg next to their names Those parameters can be changed for each time segment c To add an experiment right click the Experiment section and click Add Experiment The experiment will use those parameter entries with Expt next to their names Those parameters can be changed for each experiment d Enter the parameters for each segment and experiment When you add a new time segment the parameters for the time segment that is selected are used as the default values for the new time segment When you add a new experiment the parameters for the last experiment in the list are used as the default values for the new experiment See Chapter 3 of the Concepts Guide for an explanation of how and why you use time segments and experiments 4 Enter TOF or Q TOF MS parameter values a Click the General tab and enter any General parameters that you want to change b Click the Source tab and enter any Source values you want to change 24 c Click the Acquisition tab d Select the mode of operation for the Q TOF LC MS MS mode Auto MS MS mode or Targeted MS MS mode If you have a TOF configured you can only use MS mode Different parameters are made available depending on the mode selected e Enter any values you want to change in the Acquisition tab f Click the Ref Mass tab to set up the mass calibration g Click the Chromatogram tab to set
10. and select the correct filter set To do this select the small icon to the right of the drop down assay list circled Valid Measurements are indicated with an asterix next to them 5 Razdor Cord Tb LanthaScreen Prolacols 3 Pretocel General setting User protocis E output settnos Measurement D Lenthetersen Se Atel Label valid labels marked with A 3 Plate Optinization 3 777 wak colection Grou O Greimas w rP methods C3 Cort O Fhovescerce Intematy Le test Test Lentha FAS PractnEf ma Now Prestceloe Bottom TeShuta Check parameters er of plate recess HF Sat pite repeat eset A Meesi erent Technoiogos PE T Samples gg Barcode Settings I Reader Settings i 4 Recyde Bn 9 Alistof preloaded read protocols will appear on the left side of the screen From the list on the left click measurement technologies and method of choice If your measurement is not available in the list you can create you r own by first duplicating an existing measurement B Wallac envision Manager 1 11 Instrum F e Edi em Too Actions Heb nected Pre 0 0 2 Back Foner Lp Start f 5 Reade Control E User protocols d Lanthascracn Fi Piste Optimization Lu test Test Lantha FAS Prezzeloe New Prestofe Bottom TShota Miterbiun Tb Lerihesrem Drei b Anay ex srp i D Wallac protocol tB Rost Fi RS mentary Mi Depe
11. persons after successful training and approval Undergraduates engaged in long term independent research projects under faculty direction would be trained on these instruments upon their supervisor s request 2 Eachgroup PI will be issued an account on the system Individual operators can log into their group account with their unique password Please remember to log out of your account when finished setting up running your experiment 3 Itisthe responsibility of all users to learn the capabilities of each instrument to avoid damage and maximize efficient use of the NMR hardware For example the allowed temperature range is determined by each probe s design exceeding it may result in permanent damage 4 Forreservations go to http scheduler yale edu Please send Dr Wu or Dr Ghosh an email requesting access when you are ready to use the reservation system This has to be repeated for every new instrument you are planning to use 5 Youare responsible for using a time slot when you ve reserved it Always cancel reservations you will not use Cancellations made 12 hours before start of reserved time will not be charged 6 Allusers are encouraged to use remote stations for data analysis Of course you can use a spectrometer for data analysis if you are currently using it for acquisition Research groups are encouraged to purchase a PC workstation or Macintosh OS X 10 3 computer The core has a site license for the VnmrJ NMR softwa
12. run immediately remove all bottles from the rotor and check counterbalancing of the bottles in accordance with the manufacturer of your centrifuge Most high super centrifuges require counterbalancing within 1 0 gram Ultra speed fixed angle rotors require counterbalancing better than 0 5 gram Do not exceed maximum rotor speed under any circumstance Speed reduction may be necessary because of weight considerations of tubes adapters condition of the rotor or the density of the solution being centrifuged Be sure to follow appropriate instructions contained in the rotor manual Do not put a rotor covered with moisture on the pre cooled drive spindle or it can freeze into place Never leave the rotor on the hub for long periods Keep mating surfaces of the rotor and spindle clean If any unusual vibrations sounds or odors occur turn off power to the centrifuge immediately and do not operate the centrifuge until the cause of the improper behavior is determined Do not try to lift a rotor by force or by swaying it If not removed immediately rotors may stick to the spindles of some high speed centrifuges due to condensation that can quickly freeze over the spindle Leave the rotor in the centrifuge and wait until the centrifuge comes down to room temperature Then try lifting the rotor again Never use any abrasive tools to clean the rotor If needed uses soft brushes and wash only with mild soap or detergent solutions Also do not
13. the following menu 2 Click Add Multiple Samples 3 Enter all relevant information and click the Sample Position tab to specify the sample vial locations make sure the specific sample tray type has been configured by right clicking the autosampler device image 4 Specify the locations and click OK 5 To set up the worklist run right click the upper left corner and click Worklist Run Parameters 6 Type the paths for the method the Override DA method and the data files and click OK 7 To start the run click the Start Worklist Run icon in the main toolbar or click the Start Worklist run icon in the Worklist toolbar You can run the worklist in either locked or unlocked mode When the mode is locked no one can change the method or the worklist while the worklist is running The button in the main toolbar indicates that locked mode is on 26 NOTE To use an acquisition method that has a different DA method than the method entered in the worklist show the column called Override DA Method in the worklist by using the Show Hide Order Columns dialog box In this column type the name of another method containing the DA parameters you want to use for the sample The DA part of this method is used instead of the DA part of the current method You can also type the name of this method in the Add Multiple Samples dialog box Review results and find compounds with Qualitative Analysis Use the Qualitative Analysis program
14. up the chromatograms to plot during a run 5 Set up the data analysis parameters In the DA tab you can specify the Qualitative Analysis parameters and Quantitative Analysis parameters To set up the Qualitative Analysis parameters do the following a Click the DA tab in the Method Editor b In the Qual tab mark the Qual Automation check box c Click the Link or Copy button depending on whether you want to always use the most recent version of the Qualitative Analysis method or copy the current Qualitative Analysis method and save it to the Data Acquisition method for future use If you click Copy the method entered in the Change to Method box is copied to the Data Acquisition method when the Data Acquisition method is saved d Click the button to select the Qualitative Analysis method To set up the Quantitative Analysis parameters do the following a Click the DA tab in the Method Editor a Click the Quant tab b In the Quant tab mark the Quant Automation check box c Click the Link or Copy button depending on whether you want to always use the most recent version of the Quantitative Analysis method or copy the current Quantitative Analysis method and save it to the Data Acquisition method for future use If you click Copy the method entered in the Change to Method box is copied to the Data Acquisition method when the Data Acquisition method is saved d Click the button to select the Quantitative Analysis method Set up and ru
15. 0f21 20L 1 9 20 22 AM IB Prozos 384 Costar t 2 1 2011 2 30 17 PM No Enietacn 2 1f2011 L1148 r GFP quantification best CL 364 Costar t NA No Eniison 5 260001 8 5230 v Prezomse New 384 Costar 1 2 1 2011 12 2022PI No Enstzen 21 2011 12 17 43 PM Ip Presto Bs Bottom 384 Costar 1 amp aj25 2011 10 37 15 No Envision 9J21 2011 3 42 08 PA 3 Rash Lamp User Cp tiic Coming Lv 334 3406 3877 L 5 282011 6 5347 4 No Enivtacn SJzej2011 1 30 41 PA Fluorescein Plebe Ont mestion 164 Greiner 704008 t BINDI 2 5 SAPE No Enstson 817011 2 33 00 PM 00 exckelion apbninsoen 304 Costar L 11 4 2095 4 57 40 FI No Envision 9 10 2003 10 12 L2 AM r Predictor 384 General 1 AJ2L 2011 3 35 57 PI No Envision 7j2 jz011 11 50 15 AM 5 Cr Quent 364 Costar t J2L 201L 2 1935 PI No Entison BJ2r2011 1 36 02 PH L Copy oF Predictor I A Costar L 932012 4 30 33 P No Envtsen 8 9 2011 402125 PM Ig Fme 36 Gente a 1 NA No Enieton 5131 2011 8 10 34 AN B recitari 384 Costar t NA No Entison 60162011 2 54 08 PH Lanthescreen Eu bndr Jens Nancy t Coming Ly 384 3576 3577 L 3 zofzu1l 11 16 13 No Enstsen SJ20J201L 11 19 62 AM 4 The new protocol will open immediately 5 From the Protocol menu near the center of the screen go to General Settings and enter your plate type 28 fe gt ru BH SH RO RE 16 HH Be 6 18 E89 AD Phorescence Intensty Lo test Test Lantha FAS Lea rotated plate Use general groper height Gripper hetght Lem measurement heaght defined in label
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17. CE DELFIG Duel Mone LANCE DELF1 Dual Mone LAKKE DELFIA Dual hons LANCE JOBIG Dual onej LANCEJDELFIA Dual None LANCE Dust Mone Nons Mone LANCE OELFIG Duel More LANCE DE FLA Dual Mons LAKKEJDELFIA Hone LANCEJOELFI Duel Mone LANCEJOELFIA Duel Mone LAKKE DELFJA Cusl hons LANCEJOPUFJA Dual None LANCEJDELFIA Duel Mone Hone Money None Mone D52025 D520 25nm APC 665 APC 685 D520JESrm D zoz inm Deon APC 665 APC 665 APC B65 APC 665 Europun 615 APC Geb APC 665 APC 665 APC tez APC 665 Nore Mane ssj D456 10rm Eurcgium 615 Europium 615 D 6 10rm Europium 615 Eurepium 615 D z6 LOrM D4 8 16rm D465 10rm Europium 615 Europium 615 DHS iilh D 8 10rm DSi LNM Europium 615 Eurepium 615 Europium 615 Eurofiu 615 hone Cys 620 cys azo C y5 620 Europium 615 Europium 615 hone hone and Creston fiter ns Yes No Eris Instalsten Installation Erksen Eris Eris Tnstalation Ersin Insta atcn Installation Instalabon Instalabon Insta atcn Instalabon Instalabon Tnstalaton Erican Eris 6 20 2011 L SB 23 PM 28 2010 0 40 50 AM 9 9 2008 3110 L1 AM 9 21 2011 3 47 56 PH 20 2011 10 32 03 AM 3 3 2010 5 39 12 PM 25 2011 944122 PM 421 2001 L15405 AM 9021 2011 48 37 PH 23 2003 amp 13 37 AM 202000 13 37 AM 42112011 4 30 54 PH LOZZO L 12 24 37 M 10 23 2011 3119155 AN 6 29 2009 amp 13 35 AM 10 5 2011 6 14 38 AM 29 2008 amp 13 37 AM
18. General OVerVIGW wawo odj io e RYE o eR OY eR SR eR ACE eR NUR Adae RAIN IARE ARES ROWE 2 New Users a A AEO a eed de a an SOA A ONO eee ai 4 NMR Facility Oyerview tede te hercle AG ae aia ok 5 Usage RULES wes id 5 SCG CUMING zara kad ad dia a daw az aa Kl Waza 6 Billing wez zd A A Rod ARA A a A GiG M cde 7 Op r ation of 400A BAG 400B ao GE GE bio Gao 8 DIOEIENGBNOW RR 10 AGUEREOFECMIS err AG AE O ad ad ada RO a EGO GOA EG 11 Operation a d Sample PEP e ad L tdt vet A 11 Agilent aUi LE EO NP ILLI 12 Cleaning the ATR module essere aa aa AAAA 12 BUR SO CK AU OU AN c Z iR este I DLE A Ue tette 13 Agilent Q Tof 6550 io aEpPEDE EAZA ZZA A Ep dy t w kW 15 Agilent Q ToF 6550 tune and run SOP v1 0 2 42 ss eerte tenens 15 Envision Plate Reader a ska ii k a hak aa bb EE EEEE EErEE St 28 WCAC Ultracentrifuges and ROtOrsS as w ok aaa GLi 33 General Considerations ee eese zaa aaa aaa tern aaa tetto aaa aaa aaa aaa aa ea sets nn 33 Rotor Prep ration ssnstinin pa AA da AOS a eZ ada a as 34 What to do in case of trouble e aaa aaa aaa aaa aaa aaa aaa aaa raw aaa pa aara aaa tots stes tots stessa 35 Billing POIG so G POKO PORA ACER ZE ERO GK EGER 37 WCAC Instrument Rates FY2013 14 eeeeoo ooo oo ono esee esee e eene entente nennen nnne 38 General Overview The West Campus Analytical Core WCAC was launched in 2012 to provide the research c
19. L UE 0 000000 Y 00000 Methods have been created using a standard Mid IR configuration KBr beamsplitter Mid IR source and DTGS detector iv Choose Method Main Bench ATR from column on the left v Click on Signal monitor button SZ Resolutions Pro Multi Spectral Document Ek Fie Edi Vie lect Transforms Analysis Tools Windows Help PRS X JOWME gt te FLOW GQ Il PIEN ARE OS Drbe es 00 vl mmm Ax contents Collect AA Scan em Method Surmay Colection settings Press F1 for more help ES T Common Settings LA Background 8 Mutti Spectral Doc 1g Notes s T Background Scan Ll mmn Lond 18 Slow Kinetics E lj Signal Monitor TE Advanced Settings Summary Speed 5kHz w d 032cm sec _ z pearl asia Interferogram Sampling Interval 2 yw 5 Microscope TE Spectrometer Configuration Electronic lowpass fiter KHz 128 u p 4 Sensitivity Interferogram Symmetry Symmetric symmetric i o double sided single sided j Standard Method gt T clm E Standard Method Abs cim Restore Defaults 5 O Advanced Methods 4 Delay before collect sec o e ATR 3 5 E Microscope 3 Signal 4 auro v DualA D collect d Trigger None O Tigger out d Button start 4 4d O Tiiggerin For Help press F1 EE RE URGENT Ma 13 vi Check the voltage displaye
20. M Prezos Mew 405 photometric opt in ation 384 Costar t Enetaon 9 17 2009 3 17 92 PA Prostot Botton Burepiun Inetrogen 364 Costar t 7195 2011 2 1359 Pl No Envison 7I2GJ2011 2 13 11 PM Tohta 3 GoncB Lice Tange BLA 384 Costar 1 817 201L 24890 P No Enden BJ17 201L 2 22 51 PA i E Miror biam r SSBK PP Resh lere 364 Greirer 7040 t 1006 2009 15 21 41 1 N Eristece 1189 2009 1 57 14 P GB Res examples i m Copy of Durcpum Ler Coming Ur 399 3676 3677 L TIZYZO1L 2 55 40 FI No Eiaon TIZ5I201L 2 53 05 PM H il Wallac protocols Ig H Lotet IH Greiner 184207 L 4J28 2010 5 26 56 PI Mo Enstzen 28 2010 5 23 02 PM t D Peas m Canar Lartni onan TGG 384 Costar t 10fSf2011 12 37 551 No Emaon 10f5J2011 12 36 30 PM amp M Invertory NN Sw bosiprotocoi KH 364 Costar 1 alaena 11 56 58 No Enison 912118011 11 52 01 AM n peat NODE J E LatheccreenCebuer assay Janet JM 1230 381 No Enbtsen 10 18 20LL 2 28 34 FN RB Plates jg NN copy of Celle LarthaSa een Gom Mame lr Iho new rola 37 00 PE No Enit on 3 23 2011 4 36 22 PM Be Seres Lerkheecreen Cellier assay Flesh Lame 384 No Envison 9021 6011 4 02 37 PM Gi Barcode Settings r Genetlazer tes Jarek 304 MENEM 5 16 39 Fl No Erivtson 3Jzz 2011 3 13 35 PM 48 Resder Settings r Testa ED 1 11 96 28 No Envision 108 2011 11 31 45 AM 48 Recyde Bn i Mem Protocol 1 384 Carcal 1123 Mo Entscn Y0f20 201L 11 20 01 AM r Zot 21 EL No tison IO Z0fZ0LI 11 56 17 AM 5 Nitertium am Costar JO Ian I 9 21 13 Ma Entsen I
21. about 1 5 2psi Keep eye on plume and water droplets heading toward T joint to know when filled about 10 15 min or when meter reads 100 or when plume gets more condensed and blowing out more Once fill is complete turn off the vapor phase valve on the He Dewar remove the fill line put cap back on not too tight and insert towel back into T joint hole once the pipes warm up the clamp can be re attached to the T joint and the normal mode rube can be plugged back into the Helium port and finger tightened Lastly the meter should be changed back enter minus enter 400 NMR Pre fill fill and post fill 1 2 Loosen black cap but do not uncover Put one end of tube in helium other end to filler for magnet 40 3 Oncethe tube is ready for filling remove cap insert tube into magnet open valve and tighten the tube into magnet 4 Once filled about 15 20 min or when droplets head toward the T joint or plume blows more condensed turn vapor phase valve off on He Dewar remove the fill tube from magnet replace the cap not too tight and turn off the T valve 5 Turn the meter back to normal mode slow rate 6 Once the pipes warm up finger tighten the He port cap TURN OFF THE HELIUM CYLINDER REGULATOR NET CAPACITY NET NET 30L CAPACITY 60L CAPACITY 100L 3 5 5 3 1 3 7 3 3 1 3 4 8 7 el Te 4 12 4 2 3 5 1 2 5 5
22. appy to sit down and troubleshoot with you For periodic updates regarding the WCAC including NMR services please visit wcac yale edu You may also signup for our weekly newsletter West Campus Analytical Core Updates at https messages yale edu Subscribe Billing Users will need to provide a PATEO number when requesting access to the instruments As of May 2012 our identical walk up systems 400 MHz A and 400 MHz B the recharge rate is 5 hour based on the experiment acquisition time as measured by the instrument software For the 600 MHz system the recharge rate is 8 hour and time is accounted based on the time reserved Billing on the 400 MHz is ongoing from November 2012 billing on the 600 MHz will commence from January 2013 Faculty will be sent a copy of their usage charges on the instruments by the 5t of each month and will have till the 10t of each month to respond The charges will be submitted for billing by the 15 of the month Operation of 400A and 400B 400A Login as operator Under guest 1 Goto Protocols Tab 8 Hit Done start over 2 Click New Study for next available 3 Pick Experiment e g slot Proton 9 Logout Operator 4 Choose location from 10 Exit VNMRJ GRAY circles 11 Do not Logout remember where you guest Account placed your sample in AS Enter Sample Name Choose Solvent 7 Hit Submit pm 400B Login as operator Under walkup P 9 Go to Protocols Tab 8 H
23. b 11 Run the Check Quad Tune algorithm to check quadrupole optimization 2 to 5 minutes a Click the Autotune tab b Click the Check Quad Tune button If the Check Quad Tune results are acceptable then skip to step 14 If Checktune results are not acceptable then continue with step 12 12 Run the Quad Tune algorithm to optimize the quadrupole using all its parameters 10 to 15 minutes The source that is used must be supported for all Autotunes when running a Quad Tune The Dual ESI source is supported for all Autotunes for all instruments Refer to Supported sources for all Autotunes on page 19 for a complete list of sources that are supported for all Autotunes Also you cannot run a Quad Tune if Fast Polarity Switching is Enabled 20 a Click the Instrument State tab b For the Instrument Mode click Extended Dynamic Range c Click Apply d Click the Autotune tab e Clear the Fast Polarity Switching check box f Click Quad Tune If Quad Tune produces unacceptable results you can do an Initial Quad Tune 50 to 60 minutes If this also fails to give acceptable results please contact Terence If you would like to use custom tune parameter values you can also do a Manual Tune 13 Set the Mass Range and the Instrument Mode that you want to use to acquire data a Click the Instrument State tab b Select the appropriate Mass Range c Click the appropriate Instrument Mode d Click Apply 14 If you want to use Fast
24. d above the centerburst EVERYTIME and confirm that the voltage reads above 6 01 keep log PRSX WHE brOM I NUPJLUARKEGG BEE VA Ma Sect Quant Caitraton w EE Select Repo Temglste w C2 Select Script m Backgrou nd E hed 32scans 1 scans bsp 3s 6 422 lt 308 Parameters To run your method liquid sample 1 Choose Method Liquid ATR Ge from left column Run Background Place a drop 5 Oul of sample on the crystal Run Scan The spectrum obtained is Scan Background Save the spectra in your folder The arm does not need to be lowered for the background or liquid sample AWM PWN To run your method solid sample 1 Choose Method Main Bench ATR from left column Run Background Place the powder sample and lower the arm to ensure good contact Run Scan The spectrum obtained is Scan Background 6 Savethe spectra in your folder Alternately dissolve the solid sample in a volatile solvent place a drop onto the crystal and let evaporate Do not lower arm Ur GIN To finish Clean the crystal with KIMWIPE moistened with iso propyl alcohol Let air dry Logout 14 Agilent Q Tof 6550 This instrument is located in MIC 109 This instrument can be used with reservations only To make reservations please see Terence Wu Agilent Q ToF 6550 tune and run SOP v1 0 Start the Data Acquisition software Note e The LC modules and the LC MS instrument are turned on bu
25. en both acquisition and data analysis are done If you select to run both data acquisition and data analysis in a worklist then the data analysis method automatically follows acquisition if you mark either the Qual Automation check box or the Quant Automation check box in the DA tab in the Method Editor window You can also run a method to produce only raw data acquisition only or reprocess the data with a method containing only qualitative analysis parameters data analysis only 23 In this step you learn how to set up the method with acquisition parameters only with qualitative analysis parameters only and with a combination of acquisition parameters and qualitative analysis parameters Read and follow the instructions in the online Help for each of the tasks described on the following pages Set up a method with acquisition parameters optional If you want to download the settings to the instrument click Apply To save the method after entering parameters click either Method gt Save or Method Save As Type the name for the method in the Method field and click the OK button Set up and run a method 1 In the Context list click Acquisition 2 Enter LC parameter values Type the values for all of the LC modules configured for the instrument 3 Set up to change TOF and Q TOF MS parameters with segments and experiments a Click the TOF or Q TOF tab in the Method Editor b To add a segment right click the Time
26. ervice or pump down and restart You do not need to tune often with standard use It is recommended that you calibrate the mass axis regularly Before you run a Set Detector Gain Standard Tune or Initial Tune the Instrument Mode must be set to Extended Dynamic Range After you run one of these autotunes if you want to acquire data with a different Mass 16 Range or Instrument Mode change these values to the appropriate values for your analysis If you change the values in the Instrument State tab after you finish the autotune you must recalibrate the TOF or Q TOF If you change the mass range you must recalibrate the TOF or Q TOF You can only run Initial Tune Standard Tune Set Detector Gain Quad Tune or Initial Quad Tune with a source that is supported for all Autotunes and if the Instrument Mode is Extended Dynamic Range These buttons are grayed out if a different Instrument Mode is selected or if a different source is installed You can perform a Check Tune Quick Tune and Check Quad Tune with all instrument states and the following sources e ESI e AJS ESI Agilent Jet Stream ESI e Dual ESI e Dual AJS ESI Dual Agilent Jet Stream ESI e MMI e APPI e APCI You cannot do any of the automated tunes if the source is a nanoESI a Dual nanoESI an HPLC Chip or a MALDI source We have the dual AJS ESI source connected most of the time If Fast Polarity Switching is Enabled you cannot run any of the Quad Autotune algor
27. follow all instructions in this document The WCAC is responsible for the following three ultracentrifuges The rotors available are listed alongside Before using any instrument for the first time please notify a WCAC staff member Location BC Optima L100K ABC 216 SW 32 Ti 90Ti 70Ti 422 Ti BC Optima XE 100 MIC 312E SW 55Ti SW 28 Thermo Sorval RC6 ABC 216 Fiberlite F14 6x250y F12S 6x500 LEX F21S 8x50y SA 512 In case of a spill you should inform a WCAC staff member In addition you should immediately start appropriate decontamination procedures for the rotors centrifuge and accessories such as the vacuum pump General Considerations Never use a rotor without a lid Super speed or General Purpose rotors not tied down securely on the spindle may jump off and cause damage to the drive shaft and the centrifuge chamber Never attempt to touch or stop a rotor by hand Failure to do so may damage the surface finish of the rotor and over time expose some pointed ends of carbon filaments which may break through the skin like a wooden splinter 33 Always check prior to starting a run the condition of the segmented over speed disk of an ultra rotor The over speed disk is located at the bottom of the metallic hub If the disk is scratched partially peeled or otherwise damaged replace the disk with a new one of the same type Excessive vibration of a high speed centrifuge will indicate a grossly unbalanced rotor Stop the
28. for negative mode is necessary if you clear this check box 3 Click the Autotune tab 4 Mark the polarity to use when tuning under TOF on the Autotune tab You can mark Positive Negative or both You can also mark FastPolarity Switching If you mark the Fast Polarity Switching check box then four different autotunes are performed Positive e Negative e Fast Polarity Switching Positive e Fast Polarity Switching Negative 5 Click Check Tune to check the TOF mass calibration and optimization Then click Start Autotune Check Tune takes 3 to 5 minutes to complete You repeat Check Tune after you dilute the calibration solution if the abundances are greater than 480 000 for any of the calibrating ions for the 6550 Q TOF or above approximately 650 000 for other Q TOF and TOF instruments If Check Tune results are acceptable then you can skip to step 10 If Checktune results are not acceptable then continue with step 6 6 Click Quick Tune to use a limited set of parameters to tune the MS automatically Then click Start Autotune Quick Tune takes 7 to 10 minutes to complete 18 You repeat Quick Tune after you dilute the calibration solution if the abundances are greater than 480 000 for any of the calibrating ions for the 6550 Q TOF or above approximately 650 000 for other Q TOF and TOF instruments If Quick Tune results are acceptable then you can skip to step 11 If Quick Tune results are not acceptable then continue with step 7
29. ilute the tune calibrant before you recalibrate You recalibrate to get optimal mass accuracy 19 a Click the TOF Mass Calibration tab b Click the desired polarity in the top left corner of the Tune window To select a different set of masses click Load or select or clear individual masses in the list on the left side of the Tune window d Click the Calibrate button e If you want to calibrate the TOF analyzer in the opposite polarity repeat step b through step d 10 If you have a Q TOF instrument check the options on the Instrument State tab before you tune the quadrupole If Fast Polarity Switching is Enabled you disable it before you run any of the Quad Autotune algorithms After the Quad tune results are acceptable you will enable Fast Polarity Switching again and then recalibrate the TOF analyzer a Click the Instrument State tab b Select the appropriate Mass Range c Click the appropriate Instrument Mode d Select Disabled for Fast Polarity Switching e If you did not make any changes skip to step 14 f Click Apply g Click the TOF Mass Calibration tab h Click the desired polarity in the top left corner of the Tune window i To select a different set of masses click Load or select or clear individual masses in the list on the left side of the Tune window j Click the Calibrate button k If you want to calibrate the TOF analyzer in the opposite polarity repeat step h through step j I Click the Autotune ta
30. ingle Quad LCMS is no reservation walk up only instrument It is reserved for walk up 5 min only runs between 12 noon and 3 pm on weekdays Outside this time window long runs and batch runs are permitted To reserve the instrument for after hour runs please go to http scheduler yale edu A second computer is available in MIC109 for offline data analysis The Agilent Q Tof instrument is available for single or multiday use It can be reserved using scheduler yale edu Masshunter and MPP software suite is available on a second computer for offline data processing Currently the LCMS usage is charged at 1 00 per sample Operation and Sample Prep 7 Keep the concentration of you solvents below 1mg ml 8 Filter Filter Filter Also make sure that it is not likely to crash during the gradient run 9 Start with 2 ml injection you can always go up later 10 Solvents to stay away from Anything halogenated No CHCls CH2Cl 11 Remember to label your vial and cap it LCMS 4 If you have not used this instrument before please see Terence or Mousumi first 5 Fill in the signup sheet next to the instrument completely Also please include the method name 6 Run your method through EZAccess 7 Data can be analyzed in your lab or in a secondary computer in MIC please see Terence if you want a copy of the software 8 If you are planning long runs overnight batch runs please send out an email to let others know
31. it Done start over Click New Study for next available Pick Experiment e g slot Proton 9 Logout Operator Choose location from 10 Exit VNMRJ green circles 11 Do not Logout Guest remember where you Account placed your sample in AS Enter Sample Name Choose Solvent Hit Submit Do s and Don ts Do 1 On the 400A check for the next available slot in the software before inserting your sample The next open spot on the tray is not necessarily the next available spot 2 Wipe the spinner with a kimwipe specially the black band 3 Make sure the sample is seated properly in the sample gauge lift up and reseat if necessary NMR tube bottom should touch the platform 4 If the sample errors out you can resubmit the sample right click on the red spot and hit submit again 5 Do check to see if the yellow light comes on when the sample is inserted into the magnet 6 Do remove your samples from the auto sampler and make spinners available for other users Don t 1 Do not use the red stop button to stop an acquisition Go to Acquisition in the drop down menu and choose Abort Acquisition if you have to stop your run 2 Do not remove your samples by clicking eject stop acquisition see above and ensure that the reference sample goes back into the slot Please let a WCAC staff know if you are not able 3 Avoid edits copy and paste as it tends to hang up the software 10 Agilent Q LCMS The Agilent S
32. ith an opportunity to review current activity levels in the WCAC 37 WCAC Instrument Rates FY2013 14 Category NMR Biotechnology HPLC Mass Spectrometry Optical FACS Instrument Model Reservation Charges Yale Users Agilent DD2 400 A G8303A 400 MHz walkup 5 h Agilent DD2 400 B G8303A 400 MHz walkup 5 h Agilent DD2 600 w coldprobe Reservation 8 h Perkin Elmer EnVision 2100 walkup 20 h GE Typhoon 9000 walkup 20 h GE Typhoon 9500 walkup 20 h LAS 4000 imager walkup 20 h Agilent LCMS Q ESMS 6120B walkup 1 sample Agilent 6490 QqQ Appointment 5 sample Inert MSD DS TRURBO EI 63172A walkup 1 sample LTQ Orbitrap Velos Appointment See WCAC Staff Agilent 6550A QTOF Appointment 5 sample Agilent 1100 HPLC w UV detect Appointment 1 sample Agilent 1100 HPLC w UV detect 2 Appointment 1 sample Agilent Cary 300 UV VIS walkup 5 h Agilent Cary 660 FTIR walkup 5 h Thermo Nanodrop walkup No charge Anton Paar MCP500 walkup 5 h BD FACS Verse walkup 20 h 1 min increments BD FACS Aria Appointment 25 30 min 38 WCAC Data Storage Policy Data acquired by analytical instruments are currently stored on the instrument s hard drive and archived periodically The WCAC is in the process of creating a Data Repository for data transfer and storage that should be online by summer 2014 39 He Fill NMR Helium Fill
33. ithms Diluting the ESI L Tune Mix With the Dual AJS ESI source autotune can fail unless you dilute the tuning mix When tuning in negative ion polarity dilute the tuning mix to calibrate properly When tuning in positive ion polarity dilute the tuning mix if you are not getting proper calibration Note Quick Calibration takes approximately 1 5 minutes rather than the longer calibration approximately 15 minutes 17 Tune the TOF and Q TOF MS 1 In the Context list select Tune The Tune window appears Only the Instrument Status window the Actuals window and the Tune window are available in the Tune context Note that you tune the TOF separately from the quadrupole Initial autotunes are appropriate for initial system installations after removal replacement of ion optics or mass analyzer components or if standard tunes cannot complete successfully If you mark the Adjust the abundance for optimal calibration check box the system automatically adjusts the fragmentor voltage to reduce the abundance for calibration masses if the calibration masses are detected to be out of the 50 to 650K range If the fragmentor voltage cannot be adjusted low enough to cause the abundance level to fall below 650K the system tells you to dilute the calibrant and then to try the calibration or autotune again 2 optional For the G6550A iFunnel Q TOF clear the Always perform only Quick Calibration check box No additional dilution
34. kept clean and always lightly greased using a silicon vacuum grease e Air dry all rotor components do not wash any rotor components in a dishwasher Do not soak in detergent solutions for long periods i e overnight All rotor components including the o rings may be autoclaved at 121 C for up to an hour O rings and gaskets may be left on the rotor The rotor should be placed in the autoclave upside down Ethanol 70 or bleach 10 may also be used However ethanol disinfecting should be done away from the centrifuge at a location i e a vent hood safe for handling flammable liquids Wash all rotor components thoroughly with water to remove residual ethanol bleach or other solutions What to do in case of trouble The most common problem is spillage of sample during the run from loosely capped bottles and the resulting imbalance bent shafts and or rotor freezing over the spindle If a bottle develops a significant leak in the middle of the run there could be some damage to the drive assembly and the centrifuge chamber caused by the grossly unbalanced rotor It is strongly recommended therefore that bottles are re used only for the number of times or less if subjected to aggressive chemicals recommended by the manufacturer Do not try to lift a frozen rotor by excessive force or by swaying it If not removed 35 immediately rotors may stick to the spindles of some high speed centrifuges due to condensation tha
35. lect the protocol you want to optimize and follow the directions on the screen 31 QR 300820 tdt Rm x D Losd Reader Control EQ User protons L BED Untascreon Idle F O Piste optim atien Sclact protocol valid protocols marked with Y and cii Pur button to start tha assay 0 rhorescerce Intensty t Liz teet Tet ntis Fd i Welcome to the Assay Start Wizard Presoek Tew Prescoetos Bottom pou ThSh ts Wer bium The mord wall help you to e the seesy and nun ths required optimizations If necszeary C Ydw Aka using the werd tis possible to perform ve mus optinzations without starting the ff Color and ua ea y Frou want to perform optmeation s pisses Follow iretruchon in the wizard IF you Jost wank Co start the assay passe load the placa wth eani plas into instrumen 15 QD assy ergo dH CZ Wallac protos IF Trod current vest Color scale Logarkhmie GB Barcode Settings HE Reader Settings 2 Recyde Bn To coctus cick Mest 14 When complete your protocol will be optimized and ready to run 15 After the assay is complete please reload tray Load Button on top of screen Exit the Envision software by closing the full envision software 16 Log out of your account 32 WCAC Ultracentrifuges and Rotors This section summarizes Ultracentrifuges and rotors maintained by the WCAC and lists basic rotor and instrument maintenance tips The operator is strongly urged to strictly
36. n interactive samples 1 Click the Sample Run window 2 Enter the information such as the Sample Name the Data File Name and Path 3 Enter the Additional Information You can change the value of the parameters in the Additional Information list 25 It is now possible to run a Data Analysis method from this window by selecting Both Acquisition and DA or DA Only for the Method Type In addition you have to set Override DA method to indicate the DA Data Analysis method to execute A method can contain data acquisition parameters qualitative analysis parameters or both A Data Analysis method is a method that contains data acquisition parameters with either the Qual Automation check box marked on the Qual tab or the Quant Automation check box marked on the Quant tab 4 To start a single sample run click the Run button in the Sample Run toolbar or the Run button in the main toolbar You can run the single sample in either locked or unlocked mode When the mode is locked no one can change the method or sample parameters during a run You also cannot overwrite this data file in the Data Acquisition program The button in the main toolbar indicates that locked mode is on You can also specify an Override DA Method and select either Both Acquisition and DA or DA Only for the Method Type and then Data Analysis is run as part of the method Set up and run worklists 1 Right click the upper left corner of the worklist to display
37. nd crystal the next time it is placed on the sample The Agilent Cary 600 Series FTIR spectrometers use a helium neon laser operating in the visible region at 632 8 nanometers The spectrometer is a Class 2 laser product powerful enough to warrant caution in its use Cleaning the ATR module ii iii It is expected some residual sample will be left Much of the formed pellet can be dislodged with a wooden stick A metal spatula will be potentially too abrasive and damaging to the crystal With the remaining solid at the edges apply some isopropanol dab the top with a kimwipe and repeat this 4 5 times Also use this to scrub the general area in and around the crystal surface It is not necessary to do this for more than a second or two The solvent should not be applied in a way that the setup is soaked since it will leak into the optics as well Remember to wipe the surface of the screw above 12 FITR Operation i Login to the computer with your Yale ID amp Password LE Agilent ii Launch the Agilent Resolution Pro Software iii Click on Collect gt Method Editor Resolutions Pro Mult Spectral Document E BRSXIDWME OW OuMQ i DHOMARE OS Et f cm Sen o eT ae 5 EF aspecto 1 Standard Method XT cis E Standard Method Abe cin w C Advanced Methods w Ca TRO Ca Mevoscope 3 For Helo press F
38. ng are true you only need to recalibrate e You change the Instrument Mode in the Instrument State tab e You change the Mass Range in the Instrument State tab The peak abundances are above approximately 480 000 for the 6550 Q TOF You have to dilute the tune calibrant before you recalibrate You recalibrate to get optimal mass accuracy Typical tune mass abundances are in the range of 50 000 to 650 000 counts 1 In the Combo Bar select Tune in the Context combo box 2 Click the TOF Mass Calibration tab 3 Select the Ion Source and Polarity on the left side of the Tune window 4 To select a different set of masses click Load or select or clear individual masses in the list on the left side of the Tune window 5 Click Calibrate The TOF or Q TOF Calibration Results dialog box opens 6 optional Repeat step 3 to step 5 for the other polarity 7 Click Apply to apply the updated calibration coefficients Switch LC stream to MS After you condition the column and tune the TOF or Q TOF MS you switch the LC stream from Waste to MS a In the Context list click Acquisition b Make sure that the General tab in the TOF or Q TOF tab is selected in the Method Editor window c In the LC Stream Seg group box click MS d Click Apply Monitor MS baseline and spectral displays e If you did not monitor the LC baseline with a VWD or DAD make sure that the TOF or Q TOF baseline is stable and no spectra of interfering intensity appear
39. ommunity at West Campus with a comprehensive analytical instrumentation facility that provides access and training to a broad collection of shared instrumentation The mission of the WCAC is to support and accelerate on going research projects at both West and Main Campus and to provide suitable space for incremental additions of high value shared instrumentation Staff members train new users of instruments within the WCAC in one on one sessions All users are required to demonstrate basic knowledge of instrument operation prior to unsupervised use of the instrument Instrument usage is scheduled and monitored via a reservation website time on the instruments is charged which varies by the type of instrument and experiment The main instrumentation lab and staff is located at the West Campus Molecular Innovations Center 600 West Campus Drive room 109 with instruments also located in MIC room 310 The Advanced Bioscience Center 840 West Campus Drive and other locations on West Campus Dr Terence Wu and Dr Mousumi Ghosh are responsible for managing training users and implementing the rules at WCAC More information regarding the WCAC can be obtained by visiting http wcac yale edu The WCAC also publishes a weekly newsletter with information regarding instrument shutdowns training demonstrations and other activities Users are encouraged to sign up at https messages yale edu subscribe The WCAC also organizes regular bim
40. onthly meetings every other Fridays at 10 00 AM in MIC109 This meeting is open to users and user faculty to voice concerns and exchange ideas Below is a list of WCAC owned instruments All WCAC shared instrument are outfitted with a place card that identifies the instrument its capabilities and the contact person to request access and training Category NMR Biotechnology Mass Spectrometry Optical FACS Miscellaneous Instrument Model Location Description Agilent DD2 400 A G8303A MIC 109 400 MHz walkup Agilent DD2 400 B G8303A MIC 109 400 MHz walkup Agilent DD2 600 w coldprobe MIC 109 600 MHz Perkin Elmer EnVision 2100 MIC 310 Plate Reader GE Typhoon 9000 ABC 2nd FL CR Imager GE Typhoon 9500 MIC 310 Imager LAS 4000 imager MIC 310 Imager BC Optima XE100K MIC 312E Ultracentrifuge Sorvall RC6 ABC 2nd FL CR Centrifuge BC Optima XE100K ABC 2nd FL CR UltraCentrifuge Agilent Bioanalyzer ABC 2nd FL CR Bioanalyzer Agilent LCMS Q ESMS 6120B MIC 109 Agilent Q LCMS Agilent 6490 QqQ MIC 210 Agilent QQQ LCMS Inert MSD DS TRURBO EI 63172A MIC 109 Agient GCMS LTQ Orbitrap Velos MIC 109 LCMS Orbitrap Waters Autopure MIC109 LCMS Agilent 6550A QTOF MIC 109 dcc cue Agilent Cary 300 UV VIS MIC 109 Spectrophotometer Agilent Cary 660 FTIR MIC 109 FTIR Micro Thermo Nanodrop MIC 310 Spectrophotometer MCP 500 Polarimeter MIC310 Polarimeter BD FACSVe
41. pgraded 400 MHz Oxford Magnet operated through an Agilent console featuring DD2 technology Each 400 MHz spectrometer is equipped with an auto switchable probe Agilent OneProbe that can be tuned to 1H F 13C and P The temperature range is 80 C to 130 C The 400 MHz A instrument is equipped with a 100 slot sample changer enabling users to submit several samples at once or in queue This instrument is currently in walk up mode of operation and is meant for quick routine analyses of synthesis products This instrument is used for routine 1D H C F P The second 400 MHz instrument 400 MHz B is currently reserved for longer duration experiments It is equipped with a 12 slot sample changer for queuing up multiple experiments In addition one Agilent 600 MHz MIC room 109 triple resonance single gradient system with HCN and OneNMR probes with a 14 1 Tesla 54 mm bore Agilent Premium Compact Shield Superconducting Magnet was installed in Nov 2012 The HCN 3mm cold probe is a triple resonance probe tuned to 1H 13C and 15N with a temperature range of 0 to 80 C and can be used for proton detection and triple resonance experiments The sensitivity for proton with this probe is the best in our lab This instrument is typically reserved for long chemical and bio molecular experiments Usage Rules 1 Use ofthe spectrometers is restricted to Yale University s faculty graduate students postdoctoral fellows and other authorized
42. rcer Control zB Meeuw ort Technolo ges B terbaca B OO Fluorescence Irtensty Pucrescem Furs Wallac F1FITC Botton Te Walls PIPITC Test Plate Bekelactermeen 400 Betsclactamsse 405 bus Preskotts Peet e Gott orn estable bottom lt Ne fluorescence inter chaw fluorescence inter A C3 Fluorescence Polarization BO Lurinescence Reader Settna Recrde fin Celular LanthaSoresn artheSoren Th Earcgiun Inreferagen D34030 Es Soe 1 Copy of Lenta creen Eu Leser DAND Es Sit 1 Larihasaeen Tb Laser Ganer D340 30 Ex Sot 1 eye TT ost MH 0340 30 Es Sot 1 New LANCE Timeresobved fluonese D40 30 Ex Sot 1 LANCE Dust Laser LINZ IRF 320 LANCE Ded Laser 50 200 Lie2 TRF 320 lantheecreen ceb lar leser_anet hore Copy oF Lanthasorsen Th DMO Ex Hot 1 NE Tertir D340 30 Ex Sot 1 LANCE EujaPC Dual U2 TRF 320 Flash Lame User Opliries DO40J30 Ex Sot 1 Wallac LANCE Test Pate HTS U2 TRF 320 LANCE EuJAPC Dual Updated Lie TRF 320 Tnfont 615 As TRF 320 Homogeneous TRF Laser UN TRF 320 Homogeneous TRF U2 TRF 320 Homogeneous IRF Laer rooson UN TRF 20 walec LONCE Test Plate HTS 002 LZ CIRP 320 LANCE EujaPC Dual 662 Lie TRF 320 Moon LANCE Tmorecckwd ucrcsc fora en LANCE Tmeresc eed fluonese ire anon 1a Duel LANCEJDELFI Dual hone LAHE DEFIA Dual Mons L HCEJOE E34 Dual Mons LAKCE DELFIA Dual Mone LANCEJDELFI Dual None D yoens Mons Dances Mone LAN
43. re For offline processing you may request access to a copy vnmr software that can be installed in your laboratory 7 Seea WCAC staff member at least 1 day in advance to schedule special experiments that require long acquisition times and or setup assistance from the NMR staff Scheduling 400 MHz A with 100 slot sample changer a Monday to Friday from 8 am to 8 pm 30min max b Monday to Friday from 8 pm to 8 am unlimited time c Saturday and Sunday unlimited time 400 MHz B with 12 slot sample changer a Mondayto Friday from 9 am to 9 pm up to a maximum of 5h per user per day b Monday to Friday from 9 pm to 9 am unlimited time c Saturday and Sunday unlimited time 600 MHz http scheduler yale edu a Currently you may reserve unlimited time in 30 minute blocks with no maximum This is likely to change as use increases b Remember to alert us if you have a time sensitive sample e g degradation issues or if you are not able to reserve time all booked Other Issues Please email WCAC staff if you have issues with the NMRs and leave a note on the whiteboard in the NMR instrument room for other users if you find the instrument not functioning properly Please make use of the NMR logbook provided to write down any major or persistent issues Feel free to walk into my office and discuss any issues you are having with the instruments and any questions and suggestions you may have Terence and I are always h
44. rse MIC 113 Flow Cytometer BD FACSAria MIC 113 Cell Sorter Autoclave MIC BSMT Sterillizer Coldrooms MIC BSMT Cold Room New Users The WCAC is responsible for the maintenance of all shared equipment including those in MIC310 and ABC It is also charged with tracking usage data and metrics as well as for billing purposes It is important that new users meet with the WCAC staff prior to the first use of shared instruments so that we know who they are and are able to explain the facilities usage rules how them login procedures We request that when a new member joins a lab we are made aware of it through the departments administrative assistant so we can reach out to them and train them on the shared instruments before giving them login access Alternately the new user is welcome to email a staff member regarding interest in using an instrument and completing a Instrument Access Request Form This information is required to set up their access on the instruments NMR Facility Overview The WCAC NMR Facility currently consists of three NMR spectrometers in MIC B27 109 In the future there will be other workstations running the lab standard Red Hat Enterprise Linux and Vnmr software Currently users are welcome to install a copy of VNMRJ on their lab computers or download a free copy of Mestranova from the Universities website http cic chem yale edu mnova The WCAC operates two 400 MHz NMR spectrometers Each has an u
45. t quickly freeze over the spindle In such a case leave the rotor in the centrifuge and let the centrifuge chamber come down to room temperature Then try lifting the rotor again If that fails call the instrument manufacturer for advice and send a note to WCAC staff 36 Billing Policy Use of our three NMR spectrometers is accounted in one of two ways 1 For our identical walk up systems 400A and 400B the recharge rate is 5 hour based on the experiment acquisition time as measured by the instrument software These systems are intended for walk up use and require no advanced reservation however we encourage users to utilize the 400A for quick experiments lt 30 minutes and the 400B for longer experiments gt 30 minutes during daytime hours Both instruments are available for long experiments after 8 00 pm 2 For the 600 MHz system an on line reservation system has been implemented to schedule experiments in advance In this case the recharge rate is 8 hour and time is accounted based on the time reserved Itis worth noting that the reservations can be canceled without penalty as will be explained in the Usage Guidelines NMR Only Monthly Charges At the beginning of each month no later than the 5th you will receive a list of NMR charges incurred during the previous month You will have several days to review the pending charges after which they will be processed no earlier than the10th This is intended to provide you w
46. t the LC pump is not running To start the Data Acquisition program double click the Data Acquisition icon When Data Acquisition opens the software engines automatically start If you need to restart them right click the Acq System Launcher icon in the system tray and click Start Engines If you have recently changed LC modules remember to configure the instrument again Prepare the LC modules 1 Switch LC Stream to Waste While you condition or equilibrate the column you can tune the TOF or Q TOF MS During this time you do not want pump effluent going into the TOF or Q TOF MS so you switch the direction of the LC stream away from the MS ion source and to waste If you have the LC connected to the DAD you can still monitor the fluctuations of the VWD or DAD real time chromatogram before a run a Click the General tab in the TOF or Q TOF tab in the Method Editor window b In the LC Stream Seg group box click Waste c Click Apply Now This button only sends to the current value of the LC eluent to the instrument If you click Apply then all of the method parameters are sent to the instrument 2 Purge the LC pump 3 Condition or equilibrate the column After you purge the pump you set up to condition or equilibrate the column a Enter LC parameters and click Apply to download them to the LC 15 OR to select an LC conditioning method select one from the Method list at the top of the Data Acquisition window or from the
47. to e Review results for acquisition method development e Find compounds e Identify compounds e Do molecular feature extraction Export results e Print reports 27 Envision Plate Reader To Create your run protocol optimize and run an assay For more details please see the USER MANUAL provided 1 Login with your Yale Net ID and Password open Envision Software Manager on the computer 2 Under Protocols Create a New Folder with your name Right Click to select New Protocol 3 Follow the prompt and enter a name for the protocol click OK Hesse Tree User protocols LJ Mene Piste type umber of plates Last run Factory preset Changed by Charged gt p Test Lantha Fas Coming LY 354 3576 3577 Urlmted Na No Enitaon 1 26 2011 10 50 31 AM gt pien Europiun Laser 384 Costar t IZAL 11 40 44 No Eriviaon 9 22 2011 8 15 37 pea s D crear Tertiam Laser Coming Ur 364 3676 3677 t IAN 3 22 501 No Enstson 10202011 amp 3 FP methods Burcpiun Flzeh Larg 384 Greer 74207 L 93 zofzu1 ILIZLIGZ No Envtsen SJZOJ20IL 1120 HO wam Tertium Flash Lamp 384 General 1 10 LB BOLI 2 2 401 No Envision 1048 2011 2 28 48 PN a gt Fluorescence Intensty Celular Larthasoresey 384 General L 10 21620L1 SSS Enstscn 10YZ1 20L1 12 46 46 PM t i best Laser User Optime Coming LY 304 3570 3677 L Erison 0 17 2011 5 35 17 PM Test Lantha FAS End 384 Erare 74207 L Envtsen 101 2009 1155 25 P
48. use metal implements to remove tubes Rotor Preparation It is always important to visually inspect the rotor and its components before and after each run for unusual nicks check marks or other abnormalities Always inspect rotor seals and o rings and replace damaged o rings before use TUBE AND BOTTLE PREPARATION Check the rotor manual for specifications of bottles sealing caps and screw closures ROTOR CARE CLEANING AND DISINFECTING 34 The rotor body does not need washing and cleaning after every run However periodic washing under warm water using a mild detergent solution will help reduce the amount of salt deposits from spills and permit easy placement of sample bottles in the rotor cavities Do not use any sharp objects or tools on the rotor and any of its components Use only soft bristle brush to remove dry salts that might be deposited in the cavities or other locations unreachable by hand e The rotor contains some anodized metallic components such as the hub lid knob and tie down screw Do not allow any salts or corrosive chemicals to accumulate over these components Wash them periodically or as required after each run e Regularly check the condition of o rings Replace worn cracked or damaged o rings This rotor utilizes o rings for proper sealing of the cavities to maintain atmospheric pressure in the rotor during the run All rotor o rings and the surfaces of the o ring slots they are placed in must be

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