Axis BTA 2100D Instrukcja Operatora

Varian, Inc. 2700 Mitchell Drive Walnut Creek, CA 94598-1675/USA ©Varian, Inc. 2003-2009 Printed in U.S.A. 03-914979-00:5 Saturn® 2000 GC/MS MS Wo

8 Batch Report Printing without Recalculating ...

98 temperatures and this is okay. In general use the lowest temperature which provides acceptable chromatography. The manifold bakeout functions c

99 3800 GC System Control Window The Instrument Window Once you have configured your 3800 GC in an instrument, you may view the Instrument Window.

100 Elements of System Control Toolbar System Control Toolbar provides you with buttons to do the most common tasks performed in System Control. M

101 Multiple detectors can be viewed horizontally or vertically. The component status display can be changed to view detailed status of each comp

102 Installed hardware is listed here. The setup is changed from the 3800 GC front panel. The 3800 Setup dialog for the Saturn 2000R/3800 is al

103 Show only the chromatogram display. Continue to view the signal after the run Select the detector(s) to view. Hide/unhide the Toolbar. Set

104 Adjust zero offset. Adjust amplitude scale. Adjust time scale. Hide/unhide vertical amplitude scale slider. Documenting Module Information Yo

105 You may add and edit sections and items in sections. The injections value is updated each time an injection is performed. Select Help for det

106

107 3800 GC Injecting a Single Sample Overview By now you should have your 3800 GC configured and a basic Method built for data acquisition. If th

9 File Revision Settings ...

108 the Inject Single Sample, double-click on the vial position you wish to inject from in the carrousel display. This will bring up the Inject Si

109 Specifying Per-Sample Data Handling Parameters Most Data Handling parameters are specified in the Method used during the injection. Some param

110 Specifying a RecalcList You can choose to create a new RecalcList, append to an existing RecalcList, or not create nor update a RecalcList. To

111 List of Data Files generated in System Control, and a Quick Link button above provides access to the selected file. Automation actions and err

112 Choose the instrument for the injection. Enter information about the sample. Enter the name of the Method you wish to use. Enter the name of

113 3800 GC Injecting Multiple Samples Introduction By now you should have your 3800 GC configured and a basic Method built for data acquisition.

114 Spreadsheet columns can be sized by dragging their border using the left mouse button. Right click on the column headers for formatting optio

115 For sequentially numbered Sample names, enter the starting number and the number of entries to add to the SampleList. The Sample Names will ha

116 makes it easy to see how a Data File created with this filename specifications would appear. Specifying Per-Sample Data Handling Parameters Mo

117 If you choose to create a new RecalcList, this automatically generated RecalcList will not overwrite an existing RecalcList. If a RecalcList

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118 Click on the Carrousel button. The Carrousel dialog box is displayed. Click on the button to perform the desired operation. The SampleList is

119 List of Data Files generated in System Control, and a Quick Link button above to access the selected file. Automation actions and errors are l

120 Select Activate Method from the Sample Type cell. Click on the AutoLink button. The Activate Method dialog box is displayed. Enter the name

121 The Sequence window for the open Sequence is displayed. Enter the Method and SampleList to use. You may enter any number of Sequence lines. C

122

123 3900 GC System Control Window The Instrument Window Once you have configured your 3900 GC in an instrument, you may view the Instrument Window

124 Elements of System Control Toolbar System Control Toolbar provides you with buttons to do the most common tasks performed in System Control. M

125 Multiple detectors can be viewed horizontally or vertically. The component status display can be changed to view detailed status of each comp

126 Installed hardware is listed here. The setup is changed from the 3900 GC front panel. The 3900 Setup dialog for the Saturn 2000R/3900 is al

127 Show only the chromatogram display. Continue to view the signal after the run Select the detector(s) to view. Hide/unhide the Toolbar. Set

11 Getting Started About this Manual/Help This manual/help system contains information about how to acquire data, build methods, and operate the S

128 Adjust zero offset. Adjust amplitude scale. Adjust time scale. Hide/unhide vertical amplitude scale slider. Documenting Module Information Y

129 Select Edit Module Info. The Module Information Editor window is displayed. You may add and edit sections and items in sections. The injectio

130

131 3900 GC Injecting a Single Sample Overview By now you should have your 3900 GC configured and a basic Method built for data acquisition. If th

132 Specifying the Data File Name and Path Data File names can be up to 255 characters long. Sample ID, injection date, module name, and injection

133 Specifying a RecalcList You can choose to create a new RecalcList, append to an existing RecalcList, or not create nor update a RecalcList. To

134 The total number of injections completed is shown in the Instrument Status window. Automation actions and errors are logged in the Message Log

135 Choose the instrument for the injection. Enter information about the sample. Enter the name of the Method you wish to use. Enter the name of

136

137 3900 GC Injecting Multiple Samples Introduction By now you should have your 3900 GC configured and a basic Method built for data acquisition.

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138 Spreadsheet columns can be sized by dragging their border using the left mouse button. Right click on the column headers for formatting optio

139 When you press the Begin button, you are prompted for the Method to use. Enter the Method to use for the run……or browse for the Method file.

140 The right side of this dialog box allows you to create a filename “specification”. You can combine text entry with the “%” variable symbols sh

141 Changing Default SampleList Entries When you add a new row into a SampleList, default values are used for each cell. To change the default val

142 All Message Log entries are stamped with the time they occurred. Saving SampleLists for Later Use When you make changes to the open SampleLis

143 Enter the name of the Method to use……or pick the Method from a list of files. When this line is encountered during automated injections, the

144 Enter the Method and SampleList to use. You may enter any number of Sequence lines. Choose the action to be done in that step of the Sequence

145 System Control Menus File Menu Menu Item Description Activate Method… Displays the Activate a System Control Method File dialog box to acti

146 Menu Item Description Remember Last Open Files When checked, upon startup System Control will restore the active Method and any automation fi

147 Inject Menu Menu Item Description Inject Single Sample... Opens the appropriate Inject Single Sample Dialog Box for your system. Used to inj

13 MS Workstation Toolbar Overview Saturn GC/MS Workstation is a suite of applications for controlling chromatographs, collecting data from chro

148 Menu Item Description Reset Modules Stops the current run, resets all modules simultaneously. Automation proceeds to the next injection afte

149 Menu Item Description #:instrument name Displays the Instrument Status window and Status and Control windows for the named Instrument. i.e.

150 Menu Item Description Arrange Icons Arranges the icons, if any, in a row at the bottom of the System Control window. Sequence:, SampleList:

151 System Control Toolbar Main Toolbar The System Control main toolbar appears at the top of the Configuration and Instrument Windows. Item Des

152 Resume automation after a pause. Automation will continue at the point that it was suspended. Stop automation. Stops the current run, resets

153 2000 MS Method Basic Scan Functions Introduction The Saturn GC/MS analyzes the gas-phase ions formed from a sample in terms of their mass-to-c

154 frequency and amplitude is also applied to the endcap electrodes during the analysis to improve ion injection and unit mass resolution. The Sa

155 2000 MS Method Chemical Ionization Introduction Chemical ionization (CI) provides mass spectral data that complement electron ionization (EI)

156 The figure below shows the scan function for chemical ionization. A Reagent gas ionization, time determined by the previous scan B Ejectio

157 4. Reagent gas ions are ejected. (D) 5. The CI mass spectrum is acquired for the sample ions. (E) SECI ejects all ions above a cutoff mass b

14 Elements of the MS Workstation Toolbar Application Buttons for immediate access to the selected application. Tooltip shows the application nam

158 NOTE: Reagent ion formation can be a complex process. For example, for proton transfer CI with methane used as the reagent gas, reagent gas

159 period. The CI storage Level is typically set to a value that is lower than the mass of the reagent ion of interest. The CI Storage Level c

160 Prescan Ionization Time Prescan Ionization Time parameter as used in MS/MS applications is set to 200 sec. Default Parameters for Reagent Ga

161 CI Background Mass Set Too Low. CI Background Mass Properly Set. How to Determine the Proper Ejection Amplitude The proper setting for the R

162 Chemical Ionization Using Fixed Parameters The reaction parameters that are normally set by the Auto Control can also be set manually. For C

163 Choice of Liquid CI Reagents Many liquids may be used as CI reagents. The general requirements are a moderate vapor pressure and fairly low mo

164 Setting the Reagent Pressure for Liquid CI Reagents Connect a liquid reagent reservoir containing the chosen liquid to the liquid reagent inl

165 Adjusting the CI Reagent Gas Pressure for Gases Other Than Methane When you install a new supply of reagent gas, you must adjust the pressure

166 Reagent Ion Spectrum for Ammonia Tuning for CI Operation In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of maximu

167 The practical advantages of low-pressure CI are:  No need for an expensive vacuum pumping system to handle the large amounts of reagent gas

15 Application Buttons Used to monitor instrument status, perform automated injections, and perform batch recalculations. Used to view and edit

168

169 2000 MS Method Command Reference Spreadsheet editing Item Description Add Duplicates MS parameters of the last segment and adds it to the e

170 Item Description Segment Description Comment Line. 20 characters can be entered. Start Time Start time of segment in minutes. 0.00 to 649.99

171 Ionization Mode Item Description EI-Fixed Ions formed by electrons for a time set in method. EI-Auto Ions formed by electrons for time calc

172 Segment Setpoints Item Description Scan Time The duration of each scan (in seconds). Values from 0.10 to 5.00 seconds per scan. Below is disp

173 Ionization Mode - EI Auto Item Description Mass Range Segment Breaks The EI scan is made up of between 1 and 6 scan segments, each holding

174 Ionization Mode - EI Fixed Item Description Mass Range Segment Breaks The EI scan is made up of between 1 and 6 scan segments, each holding

175 The CI Parameters CI Auto Reagent Gas Item Description Reagent Gas Select CI reagent for application. Select User-Defined for gas not list

176 Item Description Maximum reaction time Maximum time that reagent gas ions are allowed to react with sample molecules to form ions. The maximu

177 Ion Storage (SIS) Parameters Item Description Storage Mass Ranges Table to enter ion(s) or range of ions for selective storage. Enter up to

16 Quick Link Buttons Most Recently Used Data File. A menu of operations that can be performed on the Most Recently Used Data File are displayed

178 The MS/MS Ion Prep Method Item Description Isolation Mass to be isolated and window of isolation Parent Ion Mass (m/z) Integer or exac

179 Item Description MS q Calculator Use the q Calculator for suggested excitation storage levels. Desired Product Mass Enter product mass expe

180 Item Description Isolation Time The dwell time during which the rf field is held constant in the high mass ejection step. Range 1 - 10 msec.

181 Item Description Isolation Time The dwell time during which the rf field is held constant in the high mass ejection step. Range 1 - 10 msec.

182 Item Description Excitation Storage Level Rf storage level in m/z when the dissociation waveform is applied following isolation. The excitatio

183 Item Description High Edge Amplitude Amplitude of broadband waveform used to eject masses above the isolated parent ion. Default is 30 volts.

184 Excitation Storage Level Rf storage level in m/z when the dissociation waveform is applied following isolation. The excitation storage level

185 MSn MSn uses two parent ions for sequential dissociation. The additional dissociation step can be used to increase selectivity of analyte ver

186 Item Description Waveform Type Nonresonant or resonant excitation. Excitation Storage Level Rf storage level in m/z when the dissociation w

187 Item Description Excitation Time Time for collision-induced dissociation (CID) by ion excitation. Range 0 to 1000 msec. The default is 20 mse

17 MS Workstation Toolbar Options Right-click the bar to display the Toolbar Options. A menu of MS Workstation Toolbar configuration options and

188

189 2000 MS Method Electron Ionization The Electron Ionization Scan Function with Automatic Gain Control (AGC) The ion trap has a maximum storage

190 GC peaks) the maximum ionization time of 65 milliseconds is selected, which offers maximum sensitivity. As the amount of analyte increases, th

191 The ion current measured during the AGC prescan is known as the AGC peak area. The AGC peak area is proportional to the number of ions formed

192 mass range and scan time, more than one microscan may be obtained during each scan. (The number of microscans per scan for each set of mass-ra

193 Software Parameters Segment Setpoints Scan Time The duration of each scan (in seconds). The scan time can be set to any value from 0.100 to 5

194 Mass Defect Mass defect is defined as the difference between the nominal mass of an atom (or ion) and its exact mass. Its importance arises f

195 Mass Range Segment Breaks Each EI scan is divided by default into four mass segments: 10 to 99 m/z, 100 to 249 m/z, 250 to 399 m/z and 400 to

196 Maximum Ionization Time This sets the limit for the longest ionization time which AGC can use. For maximum sensitivity, start with the defaul

197 Ionization Mode - EI Fixed When AGC is off, a fixed ionization time scan function is used to coordinate the processes that occur in the ion tr

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198

199 2000 MS Method Ion Preparation The Ion Preparation Method The two fundamental processes in mass spectrometry are ion creation and ion analysis

200 either or both segments of the scan function. Chemical ionization uses the previous scan for ion control. As shown below, the analytical scan

201 Specifying the Ion Preparation Parameters The Ion Preparation Parameters control how the basic EI or CI scan functions are modified to prepa

202 Initially, you specify the mass window of ions to be stored. Because each mass has a unique secular frequency at a given storage rf voltage, i

203 Under Storage Mass Ranges, enter the low m/z integer mass and the high m/z integer mass for each of the mass windows to be selectively stored

204 As shown below, the window of ions ejected also depends on mass. A single mass can only be ejected at low mass values. If a single high mass

205 Tips for Using SIS Observe these recommendations for best results when using the SIS application.  When selectively storing ions that are ea

206

207 2000 MS Method MS/MS Option: Theory of Operation Overview This section describes the four basic operations in Saturn Ion Trap Tandem Mass Spe

19 Launching Applications from the MS Workstation Toolbar Using the Application Icon Buttons Saturn GC/MS Workstation applications appear as icon

208 MS/MS Scan Function Parent Ion Isolation The parent ions can be completely isolated from any remaining matrix ions in another two-step proces

209 (parent ion) m/z. The m/z distribution that results from the CID process depends on the characteristics of the parent ion and the amount of en

210 multiple chemical bonds or that undergo significant rearrangements. Periodic modulation through ion resonance results in an averaging of the e

211 Note that at a storage level of 48 m/z and a CID bandwidth of 4 kHz, the mass range increases from 3 to 40 m/z when the parent ion mass increa

212 level of parent or product ions in the analytical scan results in consistent, reproducible product ion spectra. Lower target values may be req

213 Under the Isolation header, enter the Isolation Window (m/z). The full mass isolation window range is 1.0 to 14.0 m/z; the actual range is mas

214 NOTE: If the excitation amplitude used is too large, the parent ion and product ion spectra will be absent because both ions will be ejected

215 Customize Parameters window is separated into three sections. Ionization, Isolation and Dissociation. Ionization Ionization Storage Level: T

216 High Edge Offset: The integer value step to optimize the ejection of the mass just above the parent ion mass. The High Edge Offset range is -2

217 Dissociation Excitation Time: The excitation time is the time required for collision-induced dissociation (CID) by ion excitation. The excitat

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218 High Edge Offset: This parameter provides a fine adjustment for the isolation window to optimize the ejection of the mass just above the paren

219 NOTE: This value is not used if the nonresonant CID method is selected. A value of 0 gives a fixed rf storage field, i.e., no modulation Mod

220 Increase or decrease the CID (excitation) amplitude until a change in the spectra is observed. In the case of nonresonant CID, use 10 volt ste

221 Automated Methods Development Automated Method Development (AMD) is used to optimize CID conditions for product ion formation in a MS/MS met

222 It is a good idea to verify that the parent ion is isolated without a large loss in intensity. This can be done by setting the excitation amp

223 Determine the optimum rf level by plotting the product ion intensity data as a function of CID (excitation) amplitude for different rf levels

224 MS/MS You can do multiple reaction monitoring by adding lines of different parent ions masses and different dissociation parameters. The limit

225 First, work out optimized conditions for MS/MS of the first parent ion. AMD will make this process go faster. Then optimize the conditions fo

226

227 2000 MS Method Section Overview In the 2000 MS Configuration section, you configured your hardware for a 2000 and opened the System Control Wi

21 MS Workstation Toolbar Options Moving the MS Workstation Toolbar The MS Workstation Toolbar can be moved to any edge of the Windows screen. Cli

228 You will first be asked to select the instrument configuration for which you want to create a method. Select Instrument 1 for the 2000 modul

229 You will be asked to select the channels on which post-run processing will be performed. When you have selected the data channels and type(s

230 The Method Builder Window As you step down through the Method tree, the parameters associated with each section of the Method are displayed fo

231 The 2000 MS Method Windows Under the Method Directory item 2000 Mass Spec Control, click on the item MS Method Editor. The display on the righ

232 Generally, Method Segment 1 is a Filament/Multiplier Delay. This segment will be acquired with the filament and multiplier turned off to prote

233 Click on the Special Application button. From within the Special Application dialog, one may specify that data should be acquired in Profile

234 You now see additional tab dialogs for Segment Setpoints and Ionization Mode. Examine the parameters, which may be adjusted in the Segment Set

235 2000 MS Method System Control The Startup Method When you enter System Control and display the Saturn System Control Window, the Startup1.mth

236 Editing Methods from the Saturn Status and Control Window The Saturn System Control or Acquisition Window contains a "Method:" butto

237 Click on the Endtime button. Enter the new end time and click on OK. Importing Method Sections You may wish to copy sections from one Saturn

22 Move to Windows Taskbar You can display the MS Workstation Toolbar as a Windows Taskbar icon. Taskbar icons appear in the lower right (or botto

238 When the desired sections have been highlighted, click on the Import button to import them into the Method being edited. If the Method alread

239 When the desired sections have been highlighted, click on the Delete button to delete them from the Method being edited. You will prompted to

240 After a Method has been password protected, the password will be required to save changes to the Method. Once a Method is password protected,

241 3800 GC Method Command Reference 3800 GC AutoSampler When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler window may c

242 Item Description AutoSampler Type 8400, 8410, or None Specifies whether or not an 8400 AutoSampler or 8410 AutoInjector is installed on the

243 Item Description Vial I, II, or III Specifies which of the three solvent vials will be used by the Default Cleaning Volume (uL) 0 to 10.0

244 Internal Standard Section Item Description Use Yes or No If Yes, an internal standard addition will be used. When internal standard addition

245 More User Defined Settings Dialog Box This dialog box is accessed from “More User Defined…” button that is displayed when the User Defined mo

246 User Defined Settings Item Description Fill Volume (uL) 0 to 10.0 µL with 10 µL syringe 0 to 5.0 µL with 5 µL syringe Specifies the sample

247 Item Description Inject Speed (uL/sec) 0.1 to 50.0 µL per second with 10 µL syringe 0.1 to 25.0 µL per second with 5 µL syringe Specifies the

23 This dialog box allows you to select which Saturn GC/MS Workstation instrument modules are available from this Workstation. When an instrument

248 3800 GC Sample Delivery Item Description Front Valve Oven Middle Valve Oven Rear Valve Oven The 3800 GC can have up to three valve ovens inst

249 3800 GC Injector Item Description Front Injector Middle Injector Rear Injector The 3800 GC can have up to three injectors installed (front, m

250 1061 Injector Item Description Injector Oven On or off Turns the 1041 injector oven in the selected position on or off. Temperature (C) 50-

251 Item Description Rate (C/min) 1-200 ºC /min The Rate in the first row is always blank and cannot be edited. Hold (min) 0.01-999.99 min Total

252 SPT Item Description Injector Coolant On or Off Turns the coolant valve on when the SPT injection device is cooling down. The cryogenic will

253 3800 GC Flow/Pressure Item Description Front EFC Middle EFC Rear EFC The 3800 GC can have up to three injector EFC modules installed (front,

254 Item Description Pressure (psi) 0.1-100.0 psi Rate (psi/min) 0.01- 400.00 psi/min The Rate in the first row is always blank and cannot be e

255 Type 4 (for valved systems) Item Description Pressure (psi) Pressure spreadsheet 100.0 psi Rate (psi/min) 0.1-100.0 psi/min The Rate in the

256 3800 GC Column Oven Item Description Column Oven Coolant On or Off. Specifies whether or not the column coolant will be used. Enable Coolan

257 3800 GC Detector Item Description Front Detector Middle Detector Rear Detector The 3800 GC can have up to three detectors installed (front, m

24 Run Application This hierarchical menu item lists all applications showing on the MS Workstation Toolbar. When you select an item from this lis

258 FID Detector Item Description Detector Oven On or off. Turns the detector oven on or off. Electronics On or Off. Indicates whether the ins

259 TCD Detector Item Description Detector Oven On or off. Turns the TCD oven on or off. Electronics On or Off. Indicates whether the installed

260 Item Description Time Constant Slow or Fast. Carrier Gas He or N2/Argon. Filament Temp Limit (C) 390 or 490 C. EFC Type None, Type 13, Typ

261 Item Description Autozero Yes or No. Set to yes at initial time means that the TSD Autozero is on continuous before the run starts. Autozero

262 ECD Detector Item Description Detector Oven On or off. Turns the TCD oven on or off. Electronics On or Off. Indicates whether the installed

263 Item Description Methanizer Oven On or Off. Temperature (C) 450 C. PFPD Detector Item Description Detector Oven On or off. Turns the PFPD

264 Item Description Sort Sorts the spreadsheet rows by time. Photomultiplier Voltage (V) 300- 900 V. Gate Delay (msec) 20 msec. Gate Width (mse

265 3800 GC Output Item Description Port A Port B Port C The 3800 GC can have up to three output ports installed (A, B, and C). The tabs at the t

266 3800 GC Data Acquisition Item Description Detector Bunch Rate Powers of 2 from 1 to 128 points. Sets the detector bunch rate in numbers of

267 3800 GC Method Section Overview In the 3800 GC Configuration section, you configured your hardware for an instrument and opened the System Con

25 2000 MS Module Control Starting System Control the First Time Before you enter System Control for the first time, confirm that the proper instr

268 If you choose Create a New Method File, the Star Assistant Wizard will guide you in building this new method. You will first be asked to sel

269 Select the detectors for post-run processing. For each detector in the Method, you will be asked to select the channels on which post-run p

270 When you have selected the data channels and type(s) of post-run processing to be run for each detector, the Star Assistant will create a Met

271 The parameters window shows the parameters for the highlighted item in the navigation window. Method parameters are viewed and edited in this

272 The 3800 Method section contains seven Method windows: Sample Delivery, Injector, Flow/Pressure, Column Oven, Detector, Output, and Detector

273 Select rows by clicking and dragging on the row numbers on the left side of the spreadsheet. One or more rows can be selected by clicking and

274 When the Method is downloaded to the 3800 GC, component program end times that exceed the column oven end time will be truncated. Sample Del

275 Indicate whether or not you will use the installed Valve Oven by clicking on the “On” or “Off” radio buttons. Use the spreadsheet to build

276 Injector Window The Injector window contains up to three Injector Programs (Front, Middle, Rear). Use the Injector Programs to specify the tem

277 If you indicate that Coolant is turned on, specify the desired “Enable Coolant at” temperature and “Coolant Timeout”. Use the spreadsheet to b

26 Refer to the installation instructions packaged with your Ethernet card for information on installing the Ethernet card in your computer. Befor

278 You can use a spit ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to con

279 You can use a split ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to c

280 Indicate whether or not you will use the installed 1061 Injector by clicking on the “On” or “Off” radio buttons. If you indicate that a 1061

281 Flow/Pressure Window The Flow/Pressure window contains up to three EFC Programs (Front, Middle, Rear). Use the EFC Programs to specify the pre

282 The first row of the spreadsheet contains the Initial pressure and hold time for the Type 1 EFC. The EFC will equilibrate to this setting when

283 Type 3 EFC (for 1041/1061 Injectors) If you indicate that a Type 3 EFC is installed, a flow ramp spreadsheet will appear. The first row of th

284 Type 4 EFC (for Valved Systems) If you indicate that a Type 4 EFC is installed, a pressure ramp spreadsheet and a flow time program spreadshee

285 Column Oven Window The Column Oven window contains the Column Oven Program. Use the Column Oven Program to specify the Coolant Parameters and

286 Detector Window The Detector window contains up to three Detector Programs (Front, Middle, Rear). Use the Detector Programs to specify the ope

287 Indicate whether or not you will use the installed FID Detector by clicking on the “On” or “Off” radio buttons. If you indicate that an FID

27 The Network dialog box is displayed. 3. If TCP/IP is already listed in the list of network components, skip to the Note after step 5, otherwi

288 Program the Methanizer in the position corresponding to the tab in the Detector window by clicking on the Methanizer button. The Methanizer

289 If you indicate that an TCD Detector is to be turned on and heated, select the desired Temperature and Filament Temperature setting. Indica

290 Micro-TCD Detector If you indicate that a Micro-TCD Detector is installed, an Oven Power switch and an Electronics switch will appear in the t

291 TSD Detector If you indicate that a TSD Detector is installed, an Oven Power switch, an Electronics switch, a Temperature setting, a Bead Curr

292 ECD Detector If you indicate that an ECD Detector is installed, an Oven Power switch, an Electronics switch, and a Temperature setting will ap

293 PFPD Detector If you indicate that a PFPD Detector is installed, an Oven Power switch, an Electronics switch, Square Root Mode switch, and a T

294 Output Window The Output window contains up to three Output Port Programs (Port A, Port B, Port C). Use the Output Port Programs to time progr

295 Data Acquisition Window The Data Acquisition window contains instructions for collecting a baseline noise sample (Noise Monitor) and for selec

296 Autosampler Window The Autosampler window contains sampling parameters for the 8400/8410 Autosampler when attached to the 3800 GC. The paramet

297 Auto-Configuring the Method to Match the 3800 GC Hardware When you edit a 3800 GC Method while the corresponding GC is online in System Contro

1 Contents Getting Started...

28 The Select Network Protocol dialog box is displayed. 5. Select Microsoft as the manufacturer. Select TCP/IP as the protocol. Click OK. The pr

298 You are then prompted for the name of the file under which to save the Method. The active Method in System Control is updated to reflect the p

299 Once you have edited the Method and closed the Method Builder window, you are prompted to reactivate the Method. Reactivating the Method downl

300 When the desired sections have been highlighted, click on the Import button to import them into the Method being edited. If the Method alread

301 When the desired sections have been highlighted, click on the Delete button to delete them from the Method being edited. You will prompted to

302 After a Method has been password protected, the password will be required to save changes to the Method. Once a Method is password protected,

303 3800 GC System Control Command Reference Status and Control Window The 3800 Status and Control window is divided into five display areas. The

304 graphical representation of the 8400 or 8410 Carrousel. This display graphically shows which vials are to be sampled, which vials have been sa

305 Temp Zones Status Display The temperature zones status display is in the middle portion of the 3800 Status and Control window. The display in

306 Column Oven Status: Item Description Ready Yes or No. The column oven is Ready (Yes) if the setpoints have been achieved and stabilized. The

307 AutoSampler Status: This option is only shown on 3800 GCs that have an 8400 AutoSampler or 8410 AutoInjector connected to them. Item Descript

29 Enter an IP address in the range 10.2.128.1 through 10.255.255.254. Note that if you are adding more than one Workstation to this network, eac

308 Sample Delivery Status: Item Description Valve 1 through Valve 7 If the valves are configured in the 3800 GC, displays the assigned valve na

309 1177 Injector Status: Item Description Ready Yes or No. The 1177 injector oven is Ready (Yes) if the setpoints have been achieved and stabili

310 Item Description Displays the actual temperature of the 1079 injector oven at the 3800 GC. Split State On or Off. Displays the current split

311 SPT Injector Status: Item Description Ready Yes or No. The SPT injector oven is Ready (Yes) if the setpoints have been achieved and stabilize

312 Item Description Displays if a fault in the Type 1 EFC component has occurred. Type 1 Pressure Setpoint 0.1 to 100 psi Displays the programmed

313 Type 4 Injector EFC Flow/Pressure Status: Item Description Ready Yes or No. The Type 4 Injector EFC component is Ready (Yes) if the setpoint

314 Item Description Displays the TCD Range initial condition setting or the time-programmed setting in the active method. Time Const Fast (50

315 Item Description microTCD Adjustments in the active method. Current Displays, in mA, the actual microTCD current. Balance Pct Displays, in %

316 GC. Bunch Size Displays the data acquisition bunch size. Freq Displays the data acquisition bunch rate, in Hz.

317 ECD Status: Item Description Ready Yes or No. The ECD detector is Ready (Yes) if the setpoints have been achieved and stabilized. The ECD det

30 Ensure that no entries have been made in your Gateway, and that Domain Name Server (DNS) and WINS Configuration have been disabled. These entri

318 Item Description TSD Bead Power On or Off Displays the TSD Bead Power initial condition setting or the time-programmed setting in the active

319 Type 11 Detector EFC Status: Item Description Type 11 Displays the Detector EFC type. Detector EFC Type 11 has 3 channels and is used for FID

320 Type 13 Detector EFC Status: Item Description Type 13 Displays the Detector EFC type. Detector EFC Type 13 has 1 channel and is used for eithe

321 Type 15 Detector EFC Status: Item Description Type 15 Displays the Detector EFC type. Detector EFC Type 15 has 3 channels and is used for PFPD

322 8400/8410 Carrousel Display When an 8400 AutoSampler or 8410 AutoInjector is connected to your 3800, the Carrousel display will be visible in

323 Chromatogram Display Toolbar Shows or hides the toolbar. Full Scale: zooms all traces to their full scale values. This button is the same

324 Chromatogram Zooming and Scrolling The following mouse actions are possible for the chromatogram display window: Action Effect of Action Lef

325 8400/8410 Dual Mode Setup Dialog Box When the 8400 AutoSampler or 8410 AutoInjector is used in Dual Mode, this dialog box is used to assign

326 Field Description 8400/8410 Mounting Position (Informational entry only) Front or Rear When set to match the physical mounting location of th

327 Setup Ethernet Ports Dialog Box This dialog box is displayed the first time that the Star Assistant guides you through the setup of your 3800

31 Contact your Network Administrator (or whoever assigns IP addresses for your network) to see what the appropriate settings are for your Gatewa

328 Setup... Click to setup IP address management (BOOTP Server). The Setup BOOTP Server Dialog Box is displayed. Select the Workststion IP Add

329 Field Description dialog box to avoid inadvertent or unauthorized changes to IP address assignments. If this item is checked, the next time y

330 Advanced BOOTP Settings Dialog Box Item Description Assign Private Class A addresses to Hosts Manually Checked or not checked Determines whe

331 Field Description 2nd Sample Name (Dual Mode operation only)Up to 19 characters Sets the name of the second sample injected. This column is on

332 Field Description injection positions, entering the wrong position will cause the sample line to be skipped and a “Bad Injector” message enter

333 3900 GC Method Command Reference 3900 GC AutoSampler When the 8400 AutoSampler or 8410 AutoInjector is selected, the AutoSampler window may c

334 Item Description AutoSampler Type 8400, 8410, or None Specifies whether or not an 8400 AutoSampler or 8410 AutoInjector is installed on the

335 Item Description Vial I, II, or III Specifies which of the three solvent vials will be used by the Default Cleaning Volume (uL) 0 to 10.0

336 Internal Standard Section Item Description Use Yes or No If Yes, an internal standard addition will be used. When internal standard addition

337 More User Defined Settings Dialog Box This dialog box is accessed from “More User Defined…” button that is displayed when the User Defined mo

32 Configuring the 3800 or 3900 GC Communication (No Company Network) Use the following instructions if either a 3800 or 3900 GC and Varian MS Wor

338 Item Description Vial I, II, or III Selects which solvent vial to use for the solvent plug. Volume (uL) 0 to 10.0 microliters with 10 uL sy

339 Item Description Fill Volume (uL) 0 to 10.0 microliters with 10 uL syringe 0 to 5.0 microliters with 5 uL syringe Specifies the sample volum

340 Default Settings for Predefined AutoSampler Modes The following table lists the parameter settings used for each of the Predefined 8400/8410 m

341 3900 GC Injector Section 1177 Injector Item Description Injector Oven On or off. Turns the 1177 injector oven in the selected position on or

342 Item Description Time 0.00 to 999.99 min. Split State On/Off. If the split state is ON, then the sample is split according to the split rat

343 3900 GC Flow/Pressure Section Type 1 (for 1177 injector) Item Description Pressure (psi) 0.1 to 100.0 psi. Rate (psi/min) 0.01 to 400.00 ps

344 3900 GC Column Oven Section Item Description Stabilization Time (min) 10.0 min. Specifies the column Stabilization Time. Temp (C) 30 - 450

345 3900 GC Method Section Overview In the 3900 GC Configuration section, you configured your hardware for an instrument and opened the System Con

346 If you choose Create a New Method File, the Star Assistant Wizard will guide you in building this new method. You will first be asked to sele

347 For each detector in the Method, you will be asked to select the channels on which post-run processing will be performed.

33 From the Setup Ethernet Ports, click Setup for IP Address Management [BOOTP Server]. Click Setup. When the Setup BOOTP Server dialog box is

348 When you have selected the data channels and type(s) of post-run processing to be run for each detector, the Star Assistant will create a Met

349 Detailed information about the menu items and Toolbar buttons can be found in the online help. Method Notes The first item in the Method is t

350 The 3900 Method section contains two Method windows: GC Control, and Autosampler. These windows contain all parameters that control the oper

351 One or more rows can be selected by clicking and dragging on this column. Spreadsheets that specify time programs can display duplicate times

352 GC Control Window The GC control window contains sections (Flow/Pressure, Injector, and Column Oven). Flow/Pressure Section Use the EFC Progra

353 Rows after the first row of the spreadsheet contain the programmed settings for each of the ramp segments. Each segment will ramp to the speci

354 1177 Injector With a 1177 Injector is installed, an Oven Power switch, a Temperature setting and a Split Ratio table will appear. Indicate w

355 You can use a split ratio of 100 after injection to vent the injector of any residual solvent. Use a very low split ratio after flushing to c

356 Specify the desired Stabilization Time. Use the spreadsheet to build a temperature ramp program to heat and/or cool the Column Oven. The first

357 available. Selecting User Defined mode allows you access to all 8400 autosampler parameters to fine-tune your injection. Consult the Online He

34 Click the Manage IP addresses from this Workstation checkbox to manage your GC’s IP address from this Workstation. As the GC is turned on, it

358 To upload the Method from the 3900 GC to System Control, select “Upload Active Method from Modules…” from the File menu. You are then promp

359 Method… button When you click on this button Method Builder is opened with active Method loaded and the corresponding Instrument Module selec

360 import by clicking on them. If you click on one section and the hold down the shift key while clicking on another section, all of the sections

361 A dialog box of sections contained in the Method file is displayed. Highlight the sections that you wish to delete by clicking on them. If y

362 Printing the Method To print a method from Method Builder, click on the Print button on the Toolbar and select the Method section or sections

363 3900 GC System Control Command Reference Status and Control Window The 3900 Status and Control window is divided into four display areas. The

364 Item Description Runtime Shows the elapsed time in minutes since the beginning of the run. The maximum run time is 999.99 minutes. Endtime S

365 Item Description Col Oven Setpoint Abient+5 °C to 450 °C Displays the column oven programmed temperature setting in the active method. Col O

366 Item Description Stabilization Time 0.00 - 10.00 min Shows the 3900 GC column oven stabilization time in minutes. The stabilization time coun

367 Item Description Linear Velocity Displays, in cm/sec, the column linear velocity calculated from the column head pressure, column temperature

35 Click System Control/Automation. When System Control has started for the first time, the Star Assistant Communication Configuration Wizard will

368 when it is activated. It also allows the configuration of the 3900 GC to be changed from the Saturn GC/MS Workstation. Item Description Colu

369 Item Description splitless runs in which the split vent is opened.Injector EFC, Gas Saver Flow The lowest system flow rate that will be maint

370 Item Description poor operation but will not harm either the GC or the AutoSampler. AutoSampler, Syringe Speed 1 to 30 (cm/sec), default=30 T

371 Item Description Calibrate Vial 0 Position, Start Calibration To start the Vial 0 (or Vial 1) calibration, make certain a vial with the same

372 Item Description always approach the final calibration position with clockwise movements. To help facilitate this rule, the carrousel will bac

373 Item Description needle guide, so this height will give you optimum penetration depth.). Calibrate Injector Position, Start Calibration Press

374 Item Description Calibrate Vial 0 Position, Start Calibration To start the Vial 0 (or Vial 1) calibration, make certain a vial with the same

375 Item Description Calibrate Vial 0 Position, Use Mouse Buttons to Rotate Carrousel Clicking this button will display the following dialog box

376 Item Description Calibrate Injector Position, Use Mouse Buttons to Raise/Lower Syringe Using the Syringe Up button adjust the height of the n

377 Setup Ethernet Ports Dialog Box This dialog box is displayed the first time that the Star Assistant guides you through the setup of your 3900

36 From the Setup Ethernet Ports dialog box select Setup to display the BOOTP Server dialog box. Select Setup to display the BOOTP Server dial

378 Item Description Actual IP Displays the actual IP address of the connected 3900 GC. Setup... Click to setup IP address management (BOOTP Ser

379 Item Description Manage IP addresses from this Workstation Checked or not checked When IP addresses are managed from a central location by a

380 Advanced BOOTP Settings Dialog Box This dialog lets you enter advanced settings. Item Description Assign Private Class A addresses to Hosts

381 8200 AutoSampler Instrument Control Command Reference 8200 AutoSampler Status and Control Window

382 Item Description RunTime The elapsed time since the start of the run. EndTime The time when the AutoSampler Method will end. Mode Standard

383 AutoSampler Carrousel Display Item Description Black dot Indicates the vials found during Vial Check. Red fill Indicates vials listed in t

384 Hardware Dialog Box Item Description Sampling Device Specifies the size and type of syringe installed in the 8200 AutoSampler, either a 10 m

385 8200 SampleList Window Extensions When an 8200 is controlled by the Varian MS Workstation, the SampleList for that instrument contains the fol

386 Item Description Volume 0.1 to 10 ul with 10 ul syringe, or 1 to 100 ul with 100 ul syringe Sets the volume in microliters to be drawn into t

387 Carrousel Dialog Box Item Description Copy Replaces the entire SampleList with a copy of the Default Sample parameters for each vial in the

37 NOTE: If more than one Workstation is being connected on the same network, only one Workstation should manage the IP addresses for all GCs conn

388

389 8200 Method Command Reference 8200 Configuration Window Item Description Carrousel Type 12 Vials or 48 Vials Select the tray that is to be

390 Item Description Volatile Sample Used with samples in a high vapor pressure solvent. A solvent flush sampling mode with slow plunger speeds a

391 User Defined Parameters Item Description Solvent Flush Sampling When Yes is selected, the solvent plug size needs to be specified and wheth

392 Item Description Pause Time (sec) 1 to 30 seconds Sets the amount of time that the syringe will be held in the vial after the sample is drawn

393 Automated MS Report Generation Overview Once you have added Report sections to your Method, automated reports can be generated from System Con

394

395 Automation File Editor Command Reference Menus File Menu Menu Item Description New A sub-menu displays RecalcList, SampleList and Sequence.

396 Edit Menu Menu Item Description Cut Deletes a selection and copies it to the Clipboard. Used to remove or move a selected part of a spreadsh

397 Main Toolbar Item Description A sub-menu displays RecalcList, SampleList and Sequence. Selecting one of them displays the Create a New Auto

2 Specifying Per-Sample Data Handling Parameters ...10

38 When the Assign # IP addresses starting from: #.#.#.# radio button is selected, the bottom portion of the dialog changes. You may select to co

398 Open Automation File Dialog Box This dialog box is used to specify or open an automation file. The Open Automation File dialog box appears wit

399 Save Automation File As Dialog Box This dialog box is used to name an automation file. The Save Automation File As dialog box appears with sev

400 Print Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both interactiv

401 Edit Notes Dialog Box This dialog box allows you to enter descriptive notes associated with an automation file. These notes can be viewed when

402 RecalcList Window Data Files can be added to a RecalcList by clicking on a cell in the Data File column and typing the file name, or by pressi

403 Item Description AutoLink... Two AutoLink commands when Sample Type is Baseline, Analysis, Calibration, or Verification. One AutoLink comman

404 Item Description Defaults… Displays the Set Defaults dialog box, allowing you to specify default values for each applicable field in the Reca

405 Item Description Detector Channel Indicates the detector channel that is specified by the remaining fields in the row. Channels are indicated

406 Item Description Amount Standard 2-8 0.000001 to 1,000,000 Sets the amounts of the second through eighth internal standards. Used to calibrat

407 Open Data File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarc

39 The Instrument menu is displayed. Press 1 to select the Remote/ Local Control screen. The Ethernet address, IP address and Alias (which may not

408 Item Description Open File Opens the selected data file using the selected channel. Cancel Cancels file selection. SampleList Window The Sa

409 Item Description AutoLink Two AutoLink commands when Sample Type is Baseline, Analysis, Calibration, or Verification. One AutoLink command w

410 Item Description Data Files… Opens the Data File Generation dialog box to specify the naming scheme being used for Data Files generated from

411 Data File Generation Dialog Box Item Description Directory for Data Files Shows the currently selected directory where Data Files will be

412 RecalcList Generation Dialog Box Item Description Do not automatically create and update a RecalcList. No RecalcList will be generated or upd

413 AutoLink Parameters Dialog Box With AutoLink, you can specify a program to be executed after all injections of a sample have been performed, o

414 Sequence Window Item Description Action Shows the action chosen for each line in the Sequence Method Shows the Method chosen for each li

415 Automation File Editor Overview The Automation File Editor is used for editing and creation of SampleLists, RecalcLists, and Sequences outside

416 …or by clicking on the New or Open Automation File button on the toolbar. The RecalcList window for the open RecalcList is displayed. It conta

417 Editing or creating a SampleList Choose either a New SampleList or Open an existing SampleList from the File menu.. …or by clicking on the N

40 Ethernet Ports dialog box is not displayed, select the Setup Ethernet Communications menu item from the Instrument menu to display the Star Ass

418 Enter notes about the sample. Enter post-run operations to be performed. Enter information about the samples you plan to inject. Select the l

419 If you need to add several similar lines to the sample list, click on the Add Lines… button. You can then enter the common information in the

420 Specifying Per-Sample Data Handling Parameters Most Data Handling parameters are specified in the Method used during the injection. Some param

421 Specifying a RecalcList From the SampleList RecalcList… button, you can choose to create a new RecalcList, append to an existing RecalcList, o

422 Using More Than One Method for Injections The Varian MS Workstation allows you to perform automated injections using more than one Method. The

423 Editing or Creating a Sequence Choose either a New Sequence or Open an existing Sequence from the File menu... …or by clicking on the New or

424

425 GC Batch Report Overview The Batch Report application allows you to quickly generate reports for a batch of Data Files without using System Co

426 Method Selection The Batch Report application allows you to generate reports for a set of Data Files using parameters specified in a Method.

427 Generating Reports To generate reports for Data Files using the report formatting information in the specified Method drag Data Files from th

41 Adding a GC and Varian MS to the Instrument in System Control Once you have configured your Workstation computer and 3800 or 3900 GC for networ

428 The Change Application dialog box displays all post-run applications registered in the Star32.ini file in your Windows directory. The actual

429 GC Data Handling Calibration Types of Calibration There are three types of calibration available with the Varian MS Workstation: External Stan

430 Specify the calibration type. Up to 10 separate replicates. Percent of new versus historical data. Refer to the on-line help in Interactive Gr

431 Specify internal standard amounts. You can also calibrate your Method using previously collected Data Files, recalculating them as calibration

432 You may also view Calibration Curves for the active Method in Interactive Graphics. Pull down the Results menu. Select View Calibration Curv

433 Select View Curves. Generating Calibration Block Reports As you create calibration information in System Control, you may wish to generate a

434 Calibration Verification You may wish to periodically check the validity of your calibration data as you perform analytical injections. You do

435 GC Data Handling Fundamentals Introduction Even after optimizing your chromatographic conditions to provide the best separation possible, you

436 Peak Detection The Varian MS Workstation software reduces the raw data collected from the chromatograph into a results report in four steps: 

437 programs a new, wider peak width. Although it is rarely necessary, the software is also able to automatically program narrower peak width sett

42 This 3800 GC is connected to Port 44. The status indicates the availability of the GC. The IP address of the GC is shown here. Click OK, and w

438 otherwise it is considered a main peak. The rule of thumb is that the higher the programmed Tangent Percentage value, the more peaks are consi

439 Identifying Peaks Peaks are identified with the use of the Peak Table in the Data Handling section of the Method. The main purpose of the Peak

440 Calibration Curve ReportFile: c:\star\tutorial\ext std.mthDetector: ADC Board, Address: 16, Channel ID: B2-OctanoneExternal Standard AnalysisR

441 Internal Standard Calibration When you use the Internal Standard calibration type, you calibrate with regular calibration standards but you al

442

443 GC Data Handling Method Command Reference Integration Parameters Peak Detection: Item Description Subtract Blank Baseline checked or not che

444 Item Description Initial Tangent Height % 0 to 100 Sets the percentage of a mother peak's size below which a given peak is considered a

445 Peak Table Item Description Retention Time 0.001 to 1440.0 Sets the expected retention time of a peak. Specify a retention time at which yo

446 Item Description Define Peak Windows... Opens the Define Peak Windows dialog box to set time windows for reference peaks and other peaks or to

447 Calibration Setup Item Description Calibration Type % (No Calibration), Internal Standard (IS), External Standard (ES), Normalized % (N%)

43 Elements of the Configuration Screen After the 3800 or 3900 connects to System Control, configure it in an Instrument by moving its icon from t

448 Item Description Weighted Regression None, 1/n, 1/nX, 1/X2, or 1/nX2 Sets the weighted regression scheme to be used in determining calibratio

449 Item Description Edit/Lock Calibration Data... Opens the Coefficients window to edit calibration coefficients for the Method. Coefficients Tab

450 Calibration Curve Window Item Description Curve Type Shows the type of curve fit currently used. Indicates whether the curve fit has been ch

451 Item Description Revert Undoes any changes to the curve since it was last saved. Peak Name Any peak in the chromatogram Selects a peak for

452 Print All Dialog Box Item Description Curves Per Page 1, 2, 3, or 4 Lets you set how many curves will be printed on each page. Amount Units

453 Item Description Save 2 Saves overlay curve 2 as the curve for the peak. Point Info Dialog Box Item Description Exclude Selected Point from

454 Item Description Overlay Shows what the calibration curve would look like with changes to the coefficients by overlaying the new curve on the

455 Item Description Deviation Tolerance 0.0 to 500 Sets the percentage of deviation from the calibration curve beyond which a result is consider

456 Item Description Delete Deletes the highlighted Time Events Table entry from the table. Sort Sorts the table in order of increasing start ti

457 Event Description Forced Peak (FP) Forces integration between the start and end times. A resolved baseline is drawn from the amplitude of the

44 Instrument Parameters, Instrument Name, Operator Name, and Instrument status are listed here. AutoStart Module area. Place the 8200 AutoSample

458

459 GC Interactive Graphics Dialog Boxes Open Multiple Data Files Dialog Box NOTE: to quickly open files (when the file list spreadsheet is empty)

460 Item Description Look in Lists the available folders and files. To see how the current folder fits in the hierarchy on your computer, click

461 Item Description Up Moves the selected item up one row. If there is already an entry in the row above, the two entries are exchanged with eac

462 Open Method File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hier

463 Item Description Recent Files Click on this button to display a list of recently selected files. When you select a file from this list, its n

464 Save Method As Dialog Box Item Description Save in Specifies the folder into which the method is to be saved. To see how the current folder

465 Saturn Printer Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both i

466 Layout Tab Item Description Show X Axis Show or hide the time axis. Show Y Axis Show or hide the amplitude axis. Show Horizontal Scroll Ba

467 Item Description Show Offset Perspective Displays perspective lines when more than one Data File is open in overlay mode and both the time an

45 software versions (i.e. the forth software system). When the maximum number of non-fatal errors is exceeded during automation, the automation s

468 Item Description Show Peak Names When checked, displays peak names in the Main Window for all reported peaks, so even unidentified peak names

469 Item Description NOTE: all data points may not be drawn when zoomed to full or large scale. That is because the data is reduced at large sca

470 Item Description Offset by If more than one chromatogram is open, enter the amount of vertical or horizontal spacing between chromatograms. T

471 Item Description Save As … Saves the current color selection. This opens a dialog box into which you enter the name of the theme to save. Thi

472 Item Description Unidentified Peak Factor 0.00001 to 999999 Sets a calibration factor for unidentified peaks. Used to calculate results for u

473 Item Description Update List or Update Amounts Copies the current list of internal standards and their amounts from the peak table to the tab

474 Item Description Group Any integer Allows you to assign an arbitrary group number to a peak. A report can be generated organized by number. Am

475 GC Interactive Graphics Menus File Menu Menu Item Description Add/Remove Chromatogram … Opens the Open Multiple Data Files dialog box to sele

476 Menu Item Description Print Setup … Opens the Saturn Printer Setup dialog box to set preferences for printing. You can open the Print Setup

477 Menu Item Description Main Toolbar Shows or hides the main application tool bar, which contains buttons such as the Add/Remove Chromatogram

46

478 Edit Method Menu Menu Item Description Set Password … Opens the Add Password Dialog Box which allows you to add or change the password for

479 Help Menu Menu Item Description Help Topics Displays the help you are now viewing. Product Support Web Site If you have Internet access and

480

481 GC Interactive Graphics Toolbars Toolbar Overview There are two toolbars on the main window: the Main Toolbar and the Method QuickLink Toolbar

482 Reintegrate Now/Clear Moved Events: same as Reintegrate Now, except that any user defined peak start and end points are reset before reintegr

483 Previous Scaling: zooms to the previous time and amplitude range. Each time you scale chromatogram(s), Interactive Graphics adds the new scal

484

485 GC Interactive Graphics Window Locator Window Use the Locator Window to view the entire active chromatogram and to select a section of the chr

486 Main Window Use the Main Window to view and manipulate between one and seven chromatograms. This is the main window you use when working with

487 2. Show a cursor and its associated “info-panel” containing the time and amplitude of the cursor and peak information. 3. Display baselines an

47 2000 MS Instrument Control Command Reference Saturn Module Dialogs Saturn Module Keypad Dialog This dialog can be hidden by clicking on Hide K

488 You can scale vertically using the Attenuation Control to the right of the Main Window. This adjusts the amplitude range on a logarithmic scal

489 When a peak event has been moved manually, peaks whose areas are affected by the moved event are marked in the report with a ‘U‘, designating

490 Neither the position of an info-panel, nor the configured list of items are retained when the data file is closed and then reopened. These are

491 Item Description File The full path name of the active chromatogram. Channel To displayed channel of the active chromatogram. Last recalc

492 Color Type of Peak Table Entry Blue Reference peak Red Standard peak Green Relative retention time peak Yellow None of the above – a norm

493 Editing Peak Table Entries and Time Events You can later change any aspect of any time event or peak table entry by double clicking on an item

494 Info Window and Mouse Cursor Types Moving the mouse and pausing over a time event in the Visual Method Edit Window brings up a window containi

495 Action Effect of Action Right mouse button click on a peak table entry or time event. Brings up a context sensitive menu with actions to be t

496

497 GC Interactive Graphics Viewing Chromatograms in Interactive Graphics Interactive Graphics is the Varian MS Workstation application that allow

3 System Control Toolbar...151 Main Toolbar...

48 Spectrum Toolbar Click the green arrow t hide the toolbar. Click the upper left of the full screen display to restore the toolbar. Click f

498 Elements of the Interactive Graphics Window Once you have selected the file or files to view, they are displayed in the Interactive Graphics w

499 You can size and position the Locator Window anywhere on the screen. The Locator Window can be closed by clicking on the button in the upper r

500 A separate attenuation control appears for each chromatogram. When you right click on a chromatogram trace, either in overlay or tiled mode,

501 The Attenuation Control Located on the right side of the chromatogram display is an attenuation control, similar to a scrollbar which allows y

502 Toggle display of the Locator Window, the Method Quick Link button, the main Toolbar, or the Status Bar (at the bottom of the window). Toggle

503 These settings affect what additional information is displayed with the chromatogram. See the explanation of this option below. These settin

504 You may specify the colors for each of the seven possible chromatogram traces that can be displayed simultaneously in Interactive Graphics. Yo

505 If you wish to use Data Handling parameters from a Method file already stored on disk but not automatically opened when you selected the chrom

506 Select the method section you wish to open. If you wish to open the Method originally used with any chromatogram that is currently opened in I

507 When you select Build Method from Data File, you are prompted for the name of the Method file to be created. This new Method then becomes the

49 Item Description Manual Control Click the Manual Control to turn on or off the trap controls (rf, Filament, and Multiplier) and to open the CI

508 Peak Table The Peak Table is used to identify peaks so that results may be calculated. Refer to the on-line help in Interactive Graphics for d

509 This field describes acceptable values for the Value / End Time cell. Calibration Setup Calibration Setup parameters determine the type of ca

510 Edit calibration coefficients. Locked coefficients are not updated by calibration runs. Verification Setup Verification Setup options affect t

511 When you check this, peaks detected in any region that you select in the Chromatogram Display Window are automatically added to the peak table

512 To add a new time event, right-click in the Interactive Time Events window at the time where you wish the event to occur. When you right-cli

513 Moving Peak Start and End Points Peak start and end points are indicated on the chromatogram as lines or triangles (depending on the options s

514 The Reintegration List is displayed. Set the run type (analysis, calibration, verification, baseline). If you are calculating results using a

515 Viewing Results You may view results for each peak by enabling the Cursor/Peak Information display from the Chromatogram Display Toolbar. Cl

516 Viewing Calibration Curves If you are performing calibrated calculations (external standard, internal standard or normalized percent), you may

517 Double-click on a calibration point to see more information. Select the peak whose curve you wish to view. Changes made here only affect the s

50 Instrument Settings Item Description Method button Opens the Method Editor program. Segment # box Select the current segment of the active

518

519 GC Standard Report Method Command Reference Print Options

520 Single Run Reports: Item Description Title Up to 60 characters Assigns a title to the report. Print Chromatogram When checked, the Workstat

521 Results Format Item Description Units Any units, up to 10 characters Assigns a name for the units used in the results report. Number of De

522 Chromatogram Format Item Description Start Retention Time, mins 0.00 to 1440.00 Specifies a start time after injection for the chromatogram

523 Item Description Length in Pages 0 to 9 Sets the number of pages used to print a chromatogram. This option takes precedence over the chart spe

524 Item Description Chart Speed 0 .1 to 30.0 Sets the program chart speed. Attenuation 1 to 4096 Sets the program attenuation.. Attenuation is

525 Generating GC Standard Reports The Standard GC Reports Method Section Note that information about using other reporting applications such as t

526 Creates an ASCII file containing the results report. The file is named based on the Data File name and channel label, with the extension “.txt

527 Fits the high and low amplitudes to the page. Peaks inhibited with II or SR time events are ignored. When not using Auto Scale, you can time

51 Item Description Adjust Cal Gas Click to adjust the cal gas pressure. Adjust rf Ramp Change the rf setting for the instrument by turning the

528 Amount units label the X axis of the curve. Refer to the on-line help in Report for details on all fields in the Report Method section. Autom

529 Automated Printing to Multiple Printers If you are running automation on more than one instrument, you may wish to designate a separate printe

530 Batch Report Printing without Recalculating When you perform batch recalculations in System Control, reports are automatically generated using

531 Batch Printing with Batch Report You may print reports for a set of Data Files without using System Control. Click on the GC Batch Reporting

532 Click on the Standard GC Reports icon in the MS Workstation Toolbar. The Open Data File dialog box is displayed. Select the Data File. Sele

533 Specify report formatting parameters. The Data File and Method Quick Link buttons provide access to additional operations, such as reintegrati

534

535 Method Builder Dialog Boxes Create/Open Method File Dialog Box Item Description Select a method file action If Create a New Method File is

536 Open Method File Dialog Box Item Description Look in Lists the available folders and files. To see how the current folder fits in the hier

537 Item Description Notes When checked, displays any notes and/or revision log associated with the currently selected file. Open Opens the sel

52 Item Description Start Auto Tune Begins the event sequence that will tune the instrument. Only checked boxes will be executed. Reset Stops th

538 Item Description File name Shows the currently specified file. Save as type Specifies the type of file to save. Recent Files Click on this

539 Change Password Dialog Box Item Description Enter Current Password Enter the password currently used to protect the Method. Enter New Pass

540 Print Method Sections Dialog Box Item Description Sections to Print Lists the sections of the Method. Selected sections will be printed. To

541 Star Printer Setup Dialog Box This dialog box is used to specify the printers that will be used by Varian MS Workstation applications both int

542 Delete Method Sections Dialog Box Item Description Sections to Delete Lists the sections of the Method. Selected sections will be deleted.

543 Import Method File Sections Dialog Box Item Description Sections to Import Lists the sections of the Method. Selected sections will be imp

544 Select Configuration Item Description Select a Configuration Select Custom in order to add any configuration of hardware modules to the Met

545 Configure Modules Item Description Available Modules Lists the hardware modules that can be configured in the Method file. Configured Modul

546 Item Description Cancel Closes the Star Assistant. Nothing is added to the Method file. Select Detectors for Post-Run Processing Item Descr

547 Create Sections for Post-Run Processing Item Description For the following module Specifies the detector module and address for which post-

53 Item Description Electron Multiplier Voltage Manual adjustment of the Final Gain Setting determine from the Auto Tune check. SIS Amplitude Ad

548 Confirm Configuration Item Description Added Configuration Displays the hardware modules, hardware control methods, and any post-run proces

549 Method Builder Menus File Menu Menu Item Description New Starts the Star Assistant Method Configuration dialog to aid and guide you through

550 Menu Item Description Exit Closes Method Builder. If you have made any changes to the Method, you are prompted to save the changes before cl

551 Menu Item Description Tile Vertically Tiles the open Method Windows vertically (side by side). Tile Horizontally Tiles the open Method Wind

552

553 Method Builder Toolbars Overview There are three toolbars on the main window: the Main Toolbar, the Directory Toolbar, and the Window Toolbar.

554 Copies selected items to the clipboard. Pastes the clipboard contents to the selected item. Deletes selected items. If a Method section is

555 Window Toolbar When pressed, the RecalcList Generation Dialog Box pane is displayed. This pane provides a tree-structured view of the Metho

556

557 Method Builder Window Overview The Method is displayed in a window that is split into a left and a right pane. The left pane is the Method Di

54 Item Description Start Click Start to execute the desired test Reset Cancel a test executed with Start. System Test Item Description Run T

558 window from the Window menu. In addition, if you open another Method file from the File menu of Method Builder, the Method file is displayed i

559 module is expanded into the groups of editable parameters for the control method of that module. If a minus (-) sign is displayed to the left

560

561 Module Information Editor Module Information Editor Information about the hardware modules composing your instrument(s) can be maintained and

562 Entry Description PO# = 123456 Item1 = value1 SO# = A12345B Item2 = value2 Current Limitations There is no protection against duplicated se

563 Adding an Entry to a Section 1. Using the mouse or the arrow keys, select the line within the section where you want to insert a new entry.

564 Creating a Default Module Information Template New .MDF files can be created based on a template file. If MODULE00.MDF is found in the Workst

565 When you replace a hardware component, zero out (or adequately edit) the associated number of injections. You can also save free-form text by

566 confirm this deletion before it is done. File Menu The File menu contains the following commands: Item Description Save Save the contents of

567 When renaming an existing section, the name field is initialized with its current value. Type in the new name for the section. Press OK if you

55 Monitor Window Item Description Multiplier check box Display the voltage (center left) on the multiplier when on. rf check box For Service

568

569 Security Administration Overview The Security Administration window contains three window tabs that can be used to select the categories of se

570 Item Description Password for this application Allows you to specify a password required to enter the Security Administration application. No

571 Application Locking Item Description Unlocked Applications This list box shows all top level windows currently running and are not locked.

572 File Revision Settings Item Description Require Revision Log entry when changes to Methods are saved. When checked, the user is prompted for

573 Item Description Disable creation of new passwords in Method files. When checked, new passwords cannot be added to Methods. Methods already co

574

575 Standard GC Reports Command Reference File Menu Menu Item Description Open Displays the Open Data File dialog box. Print Displays the Prin

576 View Menu This menu is displayed when the chromatogram window is active. Menu Item Description Change Plot Color Displays a dialog box allow

577 Help Menu Menu Item Description Help Topics Displays the help you are now viewing. Product Support Web Site If you have Internet access and

56 Shutdown Mode Item Description Shutdown button Shuts down the system in an orderly manner. The pump speed is slowly reduced and the heaters ar

578

579 Standard GC Reports Dialog Boxes Open Data File Dialog Box Item Description Look in Lists the available folders and files. To see how the cu

580 Item Description Run Information Shows information about the currently selected file, including a thumbnail view of the chromatogram. If you a

581 Printer Setup Dialog Box Item Description Default Saturn Printer Displays the printer that is used when printing interactively from Varian M

582 Chromatogram Options Dialog Box Item Description Start Retention Time, mins 0.00 to 1440.00 Specifies a start time after injection for the

583 Item Description Initial Chart Speed, cm/min 0.0 to 30.0 Sets the initial chart speed for the printout. This speed does not change unless you

584 Item Description Attenuation 1 to 4096 Sets the program attenuation.. Attenuation is relative to the maximum full scale value of the detector

585 Notes Includes the notes you entered when you made the injection (original notes) and when you recalculated (appended notes) as part of the

586

587 Standard GC Reports Format Descriptions Results Report Below is an example of a results report generated from an analysis run. The exact forma

57 Turn OFF main power by placing switch at rear of system into OFF (down) position. Manually vent the system for at least 5 minutes using the lev

588 Title : Title Run File : Data File name Method File : Method File name Sample ID : Sample name Injection Date: Date/Time

589 [Module Run Logs] Time Events: [Data Handling Time Events] Error Log: [Module Error Logs] Calibration Report: [Calibration Report Text] Revis

590 Item Description Measurement Method section. Either Area, Height or Square Root of Height. Calculation Type Set in the Integration Parameters

591 Item Description Group This column is shown when the Show Peak Group Totals checkbox is checked in the Results Format portion of the Report M

592 Item Description The noise used by Data Handling depends upon the noise options set in the Integration Parameters Window in the Data Handling

593 Verification Report Below is an example of a results report generated from a verification run. The exact format of your verification reports m

594 9 Peak 5.580 1.0000 1.4435 44.3 5.586 -0.001 297265 --- ------------ ---------- ========== ----- ------- ======= ==

595 Standard GC Reports Toolbar Main Toolbar Displays the Open Data File dialog box. Displays the Print dialog box. Converts the text results

4 Tandem Mass Spectrometry (MS/MS)...

58

59 2000 MS Instrument Window The 2000 MS Instrument Window System Control has four major sections: the System Control Menu bar, System Control T

60 Activate Method allows you to choose a method from those already prepared. This will set the conditions for the GC, MS, AutoSampler and data ha

61 Edit Menu Click the Edit menu and highlight Edit Module Info. Each module in your system (3800GC, 2000MS, 8200 AutoSampler) contains its ow

62 Inject Single Sample Menu The command will allow you to give the sample information prior to an injection. The dialog box below will appear w

63 Automation Menu Below is a picture of the Automation pull down menu and a description of the functions. Begin Sample List will cause an automa

64 Begin RecalcList will allow you to start an automated recalculation. A recalculation list must already be prepared and selected to do this. A N

65 Instrument 1 Faults allows you to see if there are any faults in any of the modules contained in Instrument 1. An example of this screen is sho

66 Instrument 1 Status allow you to view the status of the modules connected to the system. Message Log allows you to view the event log for the M

67 In the Help dialog box, from the Index tab, you can select a particular topic. Click the selection, go to the bottom of the screen and click D

5 3800 GC System Control Command Reference...303 Status and Control Window...

68 System Control Toolbar The system control toolbar is located near the top of your screen. A picture of this toolbar is displayed below. Clic

69 Clicking on this button allows you to start a sample list that you have created. The list must already be selected. Clicking on this button

70 Spectrum Toolbar Click the arrow to hide the toolbar. Click the upper left of the screen to restore the toolbar. Click full scale to nor

71 Choosing the Chromatogram only option will allow you to see a live chromatogram as in the example below. Click Hide Keypad to expand the chrom

72 Choosing the Spectrum only will allow you to see a live spectrum as in the example below. Click hide keypad to expanded the display.

73 Click Show Keypad to display the keypad. Status and Control Window You are now ready to program the GC/MS to perform fully automated data acqu

74 You must select a method segment that is not a Filament/multiplier delay segment for the ion trap to be enabled. This method and segment select

75 The informational fields displayed in the above dialog are taken from the currently executing method. The Scan Mode describes the ionization m

76 Two filaments are provided to reduce down time for maintenance. The selection of the filament is made by choosing the radio button. The Axial

77 When the rf Modulator Response screen is displayed, it shows a real time view of the rf modulator response from 20 to 650 m/z. The vertical ax

6 Sequence Window...

78 When it is properly adjusted, the dialog will say the rf response is within limits. When you are finished, select the Done button. To adjust th

79 In CI, as in EI, the Saturn GC/MS is tuned to achieve the best combination of maximum peak height (sensitivity), optimum resolution of peaks,

80 Increase the CI gas pressure by adjusting the CI needle valve on the front of the 2000. Turn the knob clockwise to increase the pressure. When

81 Control and Status The Auto Tune methods are started from this display by clicking on the Start Auto Tune button. The method maybe stopped by

82 An example: The dialog for the air/water check is shown below. The mass 28 peak width is used to determine if air is present in the trap. The

83 Auto Tune Checks In the top center of the screen you will see 4 check boxes. These are the auto tune steps that are to be performed. If your s

84 On the left side of the dialog box is an progress bar that indicates the relative amount of AIR in the system. A message is displayed below th

85 The Electron Multiplier Tune will determine three proper settings: the Integrator Zero, the 105 gain for the Electron Multiplier and the Elec

86 sensitivity and resolution. This setting is also the value displayed in the Set Points dialog, in the Electron Multiplier voltage field. Mass C

87 is outside of these limits, check if the rf voltage amplitude is adjusted properly over the entire mass range). Straight Line Mass Calibration

7 Save Method As Dialog Box...

88 SIS Amplitude Adjust Factor. Each trap system must be adjusted for optimum ion sensitivity and ejection. See Tutorial on SIS Calibration for yo

89 Whenever you execute changes, the event log at the bottom of the screen will be updated with the time and the event that has occurred. The scr

90 The Monitor and Event Message window will detail results of the basic system. If a fault had occurred, the message would indicate what test fa

91 Also, present temperature values for each of the heating zones is displayed. Monitoring diagnostics on startup will identify any problems.

92 action will cause the heaters to be turned off and the system will begin to cool. Additionally, the turbo pump will be slowly turned off. In th

93 the cooler has warmed to the point that it won’t condense water vapor, and the pump is considered to be off. The DIFFUSION PUMP STATUS then cha

94 NOTE: The Vacuum System status should be periodically checked during Startup for foreline pressure. The pressure should read below 500 mTorr

95 In the above screen there are additional buttons which allow you to browse or check data files that already exist to make sure that you are not

96 Select one of the 3 radio buttons and name the recalculation list you are using if appropriate. In order to perform automated injections of a g

97 scanned out of the ion trap. Thus, when the multiplier gain is changed, there is no change in the actual quantity of ions formed and measured i