Thermo Ion Max
Contents
1. SI 140 GIST DART Thermo lon Max Vapur Interface User Manual Manual Revision 2 Document 7 5 063 ion sense Your source for open air mass spectrometry lonSense Inc 999 Broadway Suite 404 Saugus MA 01906 Copyright 2005 2015 by lonSense Inc All rights reserved The information in this document has been carefully checked and is believed to be reliable However no responsibility is assumed for inaccuracies Statements in the document not intended to create any warranty expressed or implied Specification and performance characteristics of the hardware and software described in the manual may be changed at any time without notice lonSense Inc reserves the right to make changes in any product herein in order to improve reliability design or function lonSense does not assume any liability arising out of application or use of any product or circuit described nor does it cover any license under its patent rights or the rights of others The apparatus and application of the apparatus described in this document is protected by US Patent Number 6 949 741 and used under license additional patents pending All trademarks are properties of their respective owners Table of Contents SCOPE Of Delivery oon ceccecccccccccseesssesssesssesssesssesssessseessesssesssesssetesneesneesteenseeneen 4 Standard System Components ccccccsecccceeceeceeceeeeeeeeseeceeseeeessueeesseeeesseeeesaeeees 4 Configuration De2. NSAI aah hr es es a hs he en es i ac he ha ch a es AT T A O ase ao ao rar ba br er aa aa a a es sb ar no a Experiment Setup Summary j he Ready Bc A A A oA oA A A oo oo sO ot os oh Os ota oso oe ote oe ot od Oe time min BT oA A A OA A A oo A oo A bi oti A A E oA oA od oot oe By A oA A oO A oo A A A A oo A oo A A A A A A oo oo A OPA a Os Os AA oo oe Oe E Time T pepe gy pe ppp sp yp Method dura 2 00 min v 0 0 1 0 2 03 0 4 0 5 0 6 0 7 08 0 9 1 1 1 1 2 1 3 14 15 16 17 1 8 19 2 9 P P PLA A oe o A A A A A A A A A A A A A A A A A A A A AAAA A A A AEA AA CA EA Oe A OA ee 5 Properties 5 Ess Properties of the method iF E Global Settings use lock ma best sho i ria a Maite C7 RA ms Properties of Targeted M E General Runtime 0 to 2 min Polarity 0 Default char 1 Inclusior 1 E ms2 Resolution 17500 AGC target 200000 Maximum IT 120 ms Isolation wir 4 0 m z Fixed first m NCE 35 0 Se eed eg eg i eg hg eg eg eg gE iia SCG hg hte eg rg hg eg rg he eg eg hed i eg eg ge Mea OCC ria a IR A Dy A cA oA Al eo A NOT SAVED 1 NOTE During the mass spectrometer instrument set up take care to set the Method Duration to a length of time matching the amount of time required to execute the DART sampling method If the Method Duration J time remains at the default of 10 minutes the data acquisition will not be
3. correct 14 Troubleshooting Pressure is too high 1 Check the vapur pump settings See the DART Vapur Pump Optimization Protocol 7 5 052 for details available on ionsense com 2 Check the ceramic tube spacing to ensure a 2 mm gap See page 8 for further details Source is open error message Check the mounting bracket alignment See page 7 for further details Maintenance No special maintenance is required for the DART Thermo lon Max Vapur Interface Replacement Parts S I 999 14 VAPUR Pump Kit 1 4 JG10019 Graphite Vespel Ferrule SI 140 CC A Contact Closure Cable SI 9xxx 47 Ceramic Tubes NOTE See VAPUR Interface Ceramic Tubes Reference Sheet 7 5 038 for ceramic tube lengths available on ionsense com Revision History Template Revision 1 Revision History DCR Description of Change Effective Date Initial Release 11 11 2013 218 Changed to Manual Template Rev 1 5 4 2015 Removed MS Instruments and flange revision from front page Added SI 140 GIST part number to front page Updated copyright date Deleted disclaimer on page 3 Deleted footer referencing part number and rev of flange Page 5 deleted 3 bullet points at the top of the page that were redundant with the text in red boxes below Deleted bolded 2mm gap comment box on page 6 Page 7 updated picture to SVP not SVP A Deleted reference and image to SVP hardware manual Updated Xcaliber Sequence set up pag
4. eye i ER S y D ae PAuL J4 ai i i hee f k N poe gt TALAT l A te ad pian lt 1 aap T pi ae ae i aS rr ga wick niet Ais Nis A N es NEST ONE oe RP Sa cit was REN ES 1 Scope of Delen Standard System Components 1 Sl 140 A SVP Thermo lonMax interface assembly for DART SVP 2 Sl 999 14 VAPUR Pump Kit 1 4 3 JG10019 Graphite Vespel Ferrule 4 SI 140 CC A Contact Closure Cable 5 SHSH_SS188_M6_12mm M6 x 12 Socket Cap Screws Configuration Dependent Components 1 Sl 9xxx 47 Ceramic Tubes 2 SI 140 INT E2 Thermo Interlock Plug Exactive 2 NOTE See VAPUR Interface _ Ceramic Tubes Reference Sheet 7 5 038 for ceramic tube lengths available on ionsense com Functional Description The DART Thermo lon Max Vapur Interface transfers the ions created by the DART source to the mass spectrometer and allows the DART source to mount on the mass spectrometer Safety Refer to the SVP Hardware and Network manual for safety warnings regarding operating the DART Installation Removing the Thermo lon Max Source Figure 2 lon Max Source Before removing the source lower the set point on the capillary temperature The temperature cannot be adjusted without a source connected Disconnect the waste hose from the bottom of the lon Max source as well as all gas syringe and voltage connections Carefully remove the lon Max source from the mass spectrometer interface and place it aside
5. in a safe place Figure 3 Thermo ion sweep cone Once the ion sweep cone Is cool enough to handle use a small flat head screw driver to loosen the set screws on the sides of the spray shield Remove the Thermo ion sweep cone as show in the photo above Figure 4 source region with the Thermo ion sweep cone removed Adjusting the Mounting Brackets Au gt z j a f k i j z d The side brackets circled in red in the photo to the left need to be adjusted before mounting the interface flange The Thermo lon Max source will fit properly even with the changed positioning of the side brackets The side brackets are generally set flush with the metal surface around the API inlet as their default factory position Figure 5 side brackets m Use a 7 64 inch Allen wrench to adjust the side brackets so that they sit just slightly towards the mass spectrometer The front surface of the brackets should be 0 2 0 3 mm back from the fount metal surface around the API inlet NOTE Remove the Thermo ion sweep cone before mounting the Vapur interface Figure 6 side bracket adjustment Attaching the Vapur Interface Figure 7 Vapur interface attached to Thermo lon Max Attach the Vapur interface to the mass spectrometer as the Thermo lon Max source mounis Lock the interface in place by turning the thumb latches on the top of the interface until they are at least 45 degr
6. e picture and instructions to be clearer 16
7. ees from the open position See the image below for detail of the thumb latches circled in red I ofore servicing Figure 8 thumb latches locked in place Inserting the Ceramic lon Transfer Tube into the Vapur Interface Remove the Swagelok nut from the front of the Vapur Interface and insert the ceramic ion transfer tube into the interface Secure the ceramic tube with one of the provided graphite Vespel ferrules making sure to set a2 mm gap between the tube and the APC Inlet Figure 9 ceramic ion transfer tube To easily set the 2 mm gap push the ceramic tube against the Thermo capillary secure the Swagelok fitting with ferrule and then mark the tube with a pencil Pull the tube out as shown in Image 3 above so that a 2 mm gap is created inside the interface Figure 10 pumping line Attach the black rubber pumping line from diaphragm pump over the barbed pumping port fitting on the side of the Vapur Interface Figure 11 DART SVP source attached to Vapur Interface Attach the base of the source directly to the bottom of the flange with the two M6 x 12 mm Socket Cap Screws provided with the flange Operation Monitoring UHV Readback on Orbitrap Systems Use of the DART source with helium will increase the Ultra High Vacuum UHV pressure readback in your Orbitrap instrument due to helium entering the highest vacuum region where the Orbitrap lies The increase in the Orbitrap pressure will not harm
8. ermo Exactive C Inspect Networking Control handler Exception while sending 09 20 15 082 Thermo Exactive Instrument s public name assigned to Exactive slot 156 do i a 09 20 24 925 Thermo Exactive C Inspect Networking Control handler Exception while sending v 09 20 24 925 Thermo Exactive Instrument s public name assigned to Exactive slot 156 lef 20 mm s Right Hs III III III DART Controls ee Connection Heater Temperature Interlock an i Analysis Graphs ta Start Erucic acid Wikipedi DART SYP Mozilla Fir J Thermo Exactive P Exactive Vacuum Pre JER OF OF L a524m vy aS Faurei 12 UHV pressure reaaback levels Ultra High Vacuum UHV pressure readback values for the Orbitrap eNitrogen is running through the DART source during this screen shot showing a low UHV pressure reading of 3 06 E 10 mbar eUHV reading will rise to approximately 9 0 E 10 to 1 1 E 9 mbar when operating the DART with helium but the system will still be stable e he threshold where the UHV will trigger a warning message is at 1 26 E 9 mbar 10 Suggested Tune File Parameters with DART lonSense recommends using the following operational settings Scan Parameters Scan Settings 1 u scan by 250 ms max inject time AGC Target Balanced 1e6 for Full MS Inlet Parameters Capillary Temp 200 C 200 C eCapillary Voltage 25 V 50 V eTube Lens Voltage 120 V 120 V Skimme
9. ffeine 100 ppb He 250C 0 5 mm s Inst Method File_ Name_009 C Xcalibur Data DART_Q Exactive_InsttMethod Caffeine 100 ppb He 250C 0 5 mm s Q Exactive Orbitrap MS File_Name_010 2 250C 0 5 mm s Not Connected Acquisition Options User crawford Instrument Start Instrument Run Rows 1 Change Instruments In Use Xi Start When Read M Instrument In Use Start Instrument Instrument Method Q Exactive Orbitrap MS Yes Start Up fOwse Shut Down f j Programs Pre Acquisition Browse Post Acquisition OWSE Run Synchronously C Pre Acquisition C Post Acquisition O2 Set System On l O Standby Off For Help press F1 NUM 10 15 2012 3 57PM NOT SAVED E G7 Windows E Al Tricks _of _Tra Presentation Inbox 1 723 Wi Thermo LTQ a i ac Agilent vapur Lon Thermo xcalb pS Ion_Max_Ion_ Q 3 58 PM Figure 14 Xcaliber sequence view 13 Xcalibur Instrument Method Set up a Untitled Thermo Xcalibur Instrument Setup aax File Help osm S x f 5 Q Exactive Orbitrap MS 5 A Scan Groups gt Targeted MS Bahasa he es er a a er er es ee lt rate Gea ea es ee AN Experiments ra es es ha he cee es be Templates System templates Full MS SIM GLO Full MS AIF Keg Full MS dd MS TopN Targeted SIM dias aa ar ba ea er ee Targeted MS eg Targeted SIM dd MS Oe Full MS AIF NL dd MS
10. pendent COMPONENIS cccceececeeeeeeeeeeeseeeeseeeeesaeeesaeeeesaaeees 4 FUNC UON MB i eld 9 6 eee enero reer ener eerrE een enne rrr ent tenner enmtrn ener rne ment ier erree ray 5 OY ce arsine ace terete A gee cise sere E E ONE E PN E E E E E 5 ULO a DO 5 Removing the Thermo lon Max Source cccccceeceeceeceeceeeeeeeeeesseeeesaeeeesaeeesaees 5 Adjusting the Mounting Brackets cccccccccseeeeseeeeeeeeeseeeeseeeeseeeeseeesseeesseeeeaeeeas 7 Attaching the Vapur Interface eciccvicrnsicandaninduaddveedessduvacicietawedssdainiadviaveiustivaneaabsenciones 8 Attaching the DART SVP source to the Vapur Interface ccccceceseeeeeeeeee ees 9 OS I EA EEA 10 Monitoring UHV Readback on Orbitrap SySteMS ccccecccseeeeeeeeeeeeeeeeeeeneeeens 10 Suggested Tune File Parameters with DART cccccesceceeeeeseeeeeeeeeeesaeeeesaees 11 ENADO Contact ClOSUl oea E EE 12 TOURIS ROOI ee E ee 15 Eea EU e E A A AE 15 Replacement Parts ccccccccscccsecceeeecececeeeceuseeseecueceueesseesueseaeesseesaeesnaeeneessaes 15 Revision History cccccceecceeeceeeeseeeceeeeseeeseeeeeueeseeeseuessueesaeeseueeseeesseesaueeseeeseeesaes 16 3 Scope of Delivery This chapter lists the components of the DART Thermo lon Max Vapur Interface gt FR P5 t lt Anew 7 S 4 gt PS s Ar vs P DER r rial tx Sas Soe e 7 et ie j UTE R a w ARI A A Mee Ar Ghee a poe Sa Pa 4
11. r Voltage 26 V 25 V eFor newer systems with the S lens design a setting of 50 is generally used NOTE On the Exactive Plus and Q Exactive only set the Capillary Temp the other parameters are not editable The following Source Parameters are set to Zero Sheath Gas Flow Aux Gas Flow Sweep Gas Flow Enabling Contact Closure Figure 13A and 13B contact closure connections Contact Closure Connections A DART SVP contact closure cable end NOTE The two wires must be positioned in positions 3 and 4 as pictured above the polarity red vs black is not critical B Thermo mass spectrometer contact closure cable end NOTE The two wires must be positioned in the Start In location under Digital signal input The polarity red vs black orientation is not critical Xcalibur Sequence Set up 1 Select a single line or highlight the whole sample queue for submission 2 Click on the Run Sample or Run Sequence button in the Sequence view to begin the MS instrument data collection set up 3 Click on Change Instruments in the Run Sequence dialog box in order to check that the mass spectrometer is not selected to initiate the data acquisition 4 The mass spectrometer setting must be as shown here Start Instrument should not be selected by any installed device NOTE Deselect a device by clicking over the Start Instrument zone for any devices that are selected Ye
12. s for Start Instrument and it will no longer be selected 5 Leave this setting to On If you select Standby you may experience issues with sequence hang ups 6 Click Ok to submit your Sequence 7 After clicking OK in the Run Sequence dialogue box you will see that under the instrument name in the Status panel that the instrument will read Waiting for Contact Closure At this point the mass spectrometer is ready and waiting for an input signal Navigate to the DART SVP control software to begin the analyses a m7 DWE amp B gt M I 30 EHN File Name Path Inst Meth SampleName Comment on Queue ame_001 C Xcalibur D ata DART_Q Exactive_InstrMethod Caffeine 100 ppb He 250C 0 5 mm s Run Manager Name_002 C Xcalibur Data DART_G Exactive_InstMethod Caffeine 100 ppb He 250C 0 5 mm s Check Devices lle_Name_003 C Xcalibur Data DART_G Exactive_InstMethod Caffeine 100 ppb He 250C 0 5 mm s Sequence File_Name_004 C Xcalibur D ata DART_O Exactive_InstrMethod Caffeine 100 ppb He 250C 0 5 mm s Sample Name File_Name_005 C Xcalibur Data DART_Q Exactive_InstMethod Caffeine 100 ppb He 250C 0 5 mm s Working On File_Name_006 C Xcalibur Data DART_Q Exactive_InstrMethod Caffeine 100 ppb He 250C 0 5 mm s Position File_Name_007 C Xcalibur D ata DART_O Exactive_InstiMethod Caffeine 100 ppb He 250C 0 5 mm s Raw File File_Name_008 C Xcalibur Data DART_Q Exactive_InstiMethod Ca
13. the mass spectrometer or cause it to function differently Below is a screenshot showing what the Thermo Orbitrap s UHV pressure readback level normally would be dd Thermo Exactive DART Default Positive Method Peripheral Devices Syringe pump no communication File Windows Help EPB ssf Weyer t Spectrum F Instrument Status Instrument Peripheral Instrument Control RRR RTRA RE ee 888358 RT Scan 4188754 uS 1 IT 20 0 NL 8 64E4 ello Type FTMS p NSI Full ms 75 00 800 00 Evaluate Current Scan System Analysis Graph Performance Warns Electronics Nt Vacuum ds Bakeout 4 Peripheral Devices Syringe pump ccc Ion source J Vacuum Bakeout am Ok HY Fore vacuum mbar 1 71E 00 1 71e 00 mbar 3 Fore Vacuum High vacuum mbar 3 03E 05 High Yacuum 3 03e 05 mbar UHY mbar 3 06E 10 60 Ultra High Yacuum 3 06e 10 mbar Source TMP Speed 100 al ae cee UHY TMP Speed 100 alt lt i ees Enter standby after Bakeout Relative Abundance 0 0 ston j DARI SYP Mozilla Firefox Sek tal Mi tli ble J LL a 100 200 300 400 500 600 700 800 m z 199 108 ED http 192 168 10 111 index htm Sense DART ap Linear Rail Controls Priority Source Time a Description 09 20 01 709 Tune startup x 09 20 15 081 Th
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