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<p>Here are possible causes and solutions:<br/> -System was vented because of a main power failure: A main power failure has the same consequence as switching off with the main power circuit breaker switch. If the power is available again, the system is started up automatically: the pumps are switched on and the vacuum is created. If the system has been vented during the mains failure, it is necessary to bake out the system to obtain the operating vacuum. See “Baking Out the System” on page 8-12 of the manual. If the log file of the data system shows a reboot of the system and the pressure reading in the Tune software shows a bad vacuum, this indicates that the system was vented. In case of frequent but short power failures, we recommend that you install an uninterruptible power supply (UPS). If main power failures occur frequently while the system is not attended (for example, in the night), we recommend that you install a power fail detector. - Vacuum leak: Refer to pages 7-5 and 8-12 in the Operator's Manual (https://assets.thermofisher.com/TFS-Assets/CMD/manuals/man-bre0012255-exactive-series-manbre0012255-en.pdf). <br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>Clogging of the H-ESI spray needle is generally caused by the presence of non-volatile components in the injected samples. If the non-volatile components of the samples are not removed during sample preparation, they will be injected onto the column where they will gradually bleed off over time into the detector. They may also be directly introduced by the use of non-volatile buffers in the mobile phase. Non volatile buffers should be avoided in LC-MS analysis because the spray needle will clog frequently and in addition the MS optics will quickly become contaminated.<br/><br/> Clogging issues may be worsened when using a divert valve or bypass valve. This is because when the valve switches to waste the LC flow to the needle is stopped, causing the residual liquid in the hot needle to quickly evaporate. This in turn causes the non-volatile components to deposit on the inner wall of the tubing which will eventually clog it.<br/><br/> When using a divert or bypass valve, the issue may be fully resolved by adding another HPLC pump to supply make-up flow through the needle when the column eluent is bypassed. The second pump is connected to the divert valve or bypass valve so that when the eluent is diverted to waste, clean solvent flows through the needle to help keep it clean. Alternatively, sample preparation procedures should be modified to reduce the amount of non-volatile components in each sample injection. <br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>The HCD Cell consists of a straight multipole (octapole) device mounted within a metal tube. The metal tube is in turn connected to the C-Trap in direct line of sight.<br/><br/> The voltage offset between the C-Trap and the HCD Cell is used to accelerate the precursor ions into the gas filled cell. Inside the HCD cell, ions collide with the neutral gas causing rotation, stretching and ultimately cleaving bonds to create fragment ions and neutral species, which are subsequently removed by the vacuum system.<br/><br/> The generated fragment or product ions are then pushed back toward the C-Trap and focused before being pushed toward the Orbitrap analyzer. <br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>AGC stands for Automatic Gain Control.<br/><br/> The Automatic Gain Control alters the number of ions in the Orbitrap by filling the C-trap for a calculated period of time. This way, ions can enter the mass analyzer at specified times only.<br/><br/> The ions are gated in the C-Trap and compressed into a narrow cloud before being pushed out to the Orbitrap. The AGC is calculated and during the injection time is when the ions can pass into the C-Trap. Hence, Ion “gating” occurs by changing the polarity of the split lens after the first multipole.<br/><br/> Depending on the experiment and other instrument parameters, the AGC is calculated in three different ways:<br/><br/> AGC Calculated with a Prescan:<br/> When the system is performing the first scan of the run, the instrument will perform a Prescan to calculate the number of ions at that time and to adjust the injection time for the analytical scan accordingly. This is achieved by opening the trap for 1 ms and by performing an acquisition in the Orbitrap (~200 ms).<br/><br/> AGC Calculate on a Scan-to-Scan basis: When two consecutive full scans are acquired within 400 ms, the instrument will use the previous Full Scan TIC to adjust the injection time.<br/><br/> pAGC (predictive AGC): When the method is setup to perform data dependent MS experiments, the dependent scans will use their master scan (Full Scan) as a reference for the AGC calculation. <br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>Yes, it is possible to work in polarity switching mode. The switching time is about 250 ms. With a resolution of 35,000 it takes about 1 s for a cycle of one positive and one negative scan (data point).<br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>Mass calibration should be performed daily by default. If the lab qualified the instrument in their controlled conditions, weekly calibration is fine. System calibration should be performed monthly. Generally, we specify less than 3 ppm mass deviation within 24 hr.<br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>In PRM, you can choose a lower resolution because of the selectivity of MS2 ions.<br/><br/> If you need to do polarity switching in Full Scan mode, it is a good idea to reduce resolution to 35,000 to generate more data points. However, this might generate less data points.<br/><br/> If you want to work qualitatively, you might want to consider to work with lock masses and the highest resolution (fine isotopic pattern). View table <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center/liquid-chromatography-mass-spectrometry-instruments-support/exactive-plus-orbitrap-mass-spectrometer-support/exactive-plus-orbitrap-mass-spectrometer-support-getting-started.html?open=g4#g4">here</a> for suggested resolution settings.<br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>

<p>AGC targets of Full Scan: 1 x 10E6 and SIM/PRM: 2 x 10E5 are good starting points. The more similar the ions that are collected in the C-trap are, the lower the target should be.<br/><br/> Max IT: <p>View table <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center/liquid-chromatography-mass-spectrometry-instruments-support/exactive-plus-orbitrap-mass-spectrometer-support/exactive-plus-orbitrap-mass-spectrometer-support-getting-started.html?open=g3#g3">here</a> to see the scan times required for the different resolution settings.<br/><br/> In the simplest case, set the max IT to times just below these values - parallel acquisition.<br/><br/> In Full Scan mode, usually the defined max IT time is not used by the system as the ion flux is very high. In data dependent MS2 scans, the time can be extended to receive a better spectrum quality. However, this might generate less data points.<br/><br/>Find additional tips, troubleshooting help, and resources within our <a href="https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/mass-spectrometry-support-center.html?icid=faqsc39">Mass Spectrometry Support Center</a>.</p>