ESI-TOFMS instructions, when using the syringe pump
Background Information
The TOFMS is used to obtain an accurate mass 
To obtain an accurate mass you must calibrate the mass axis before you run your samples and use an internal standard during the analysis of your samples
The TOFMS is a very sensitive instrument and sample concentration should be around 1 microgram/ml
Solvents for ESI-TOFMS: acetonitrile, water, methanol, ethanol, propanol, isopropanol.
You can add a matrix modifier to enhance the formation of positive ions: acetic acid, formic acid, trifluoroacetic acid (less than 0.01% - TFA is used mostly to improve chromatography) or ammonium formate (10 mM or less), ammonium hydroxide for negative mode. 10% IPA has been shown to increase negative ion formation.
Do not use any non-volatile salts in the your solvents. Do not use inorganic acid in your solvents, this will cause ion source corrosion.
You use the program Data Acquisition to calibrate and acquire data on the instrument and the program Qualitative analysis to analyze your data. There is also another program Isotope Distribution Calculator that can predict isotope patterns given a formula.

Calibrating the mass axis (the x axis): this should be done daily
There are two solution bottles in the instrument one labeled A and one label B. The A bottle contains reference/internal standard solution and the B bottle contains calibration/tuning solution (for ESI use ESI-L low concentration tuning mix G1969-85000, use it straight, do not dilute). Check these two bottles before you start your work to make sure there is solution in both bottles.
Launch the Data Acquisition software
First Calibrate the Instrument
Under Context switch to Tune. Always say No to any questions about saving a Layout or saving anything else, always save what you want manually.
Turn on the TOFMS by right clicking on the TOFMS icon group and select On.
Wait for the software indicator icon to turn green. (green = ready, yellow is not ready yet, red = some sort of error occured)
Select the radio button for bottle B under Calibrant bottle and wait for the system to become ready again as indicated by the green ready status icon.
On the tab TOF Mass Calibration tab click the Calibrate button. Wait for the calibration routine to finish and then assess the quality of the calibration. General anything less than +/- 2 ppm is good.
Select the radio button for None under Calibrant bottle.
Under Context switch to Aquisition. Always say No to any questions about saving but yes to proceeding.

Then Run your Sample
Side note: After you've switched the context back to Acquisition at the lower left hand corner click on the Method Editor tab from there click on the General tab on the tab group in the center of the screen. On the General tab there is a icon group called LC Stream (Seq) with two radio buttons marked MS and Waste.  MS sends any flow coming in to the side of the mass spectrometer (from either the HPLC or syringe pump) to the ion source and Waste sends any flow to waste. Sometimes the instrument will switch to waste (you hear the diverter valve switch) but the radio button has MS is still been shown as selected, you'll need to click Apply and Apply Now buttons to get the valve to switch back so your solvent flow will be directed into the ion source. 
Load in the desired method (top of the screen toolbar around the middle of the screen). For syringe based work generally you're going to want to use the ESI_POS.m method.
Load a syring full of your sample and insert it into the syringe pump.
Set the pump to the desired speed. Press the  Select button twice on the syringe pump to get into the rate change mode. Use the left and right arrow keys to change the pump rate then press the Select button once to get the syringe pump back into normal operation mode. Flow rates between 600 and 1200 microliters/hr are fine. You'll set the flow rate depending on the what the TIC (total ion chromatogram and ion intensity looks like). You want you're TIC to be at a fairly constant level throughout the run (dips could be irratic nebulization or air bubbles) and you want you intensity to be less then 1 million counts. Ideally sample intensity should be around 100,000 counts but anything between 50,000 and 500,000 counts is acceptable. DO NOT LET YOUR ION COUNTS EXCEED 2 MILLION COUNTS, if they do stop the syringe pump, clean out the syringe and flush the system (you may also need to recalibrate the instrument).
Press the Run/Stop to start the syring pump running. A flashing arrow indicates the syringe pump is running.
Now wait for your sample peak to appear in the real time window. Once you see your sample peaks start the reference bottle pumping by going to the Ref Mass tab and clicking the Apply Now button then the Apply button making sure that both Enable and Use Bottle A are checked on that page.
Once you see the reference peaks and your sample peak then you're ready to acquire data. Go to the Sample Run tab (located at the bottom left of the window) and fill in both spots for name and select your Path to your data folder on argenta (the z drive on the computer). Finally click the black triangle play button to start data collection.
Once your sample is done click the View Data button on the Sample Run tab to open Qualitative Analysis program with your current data set pre-loaded.
Also at this point start cleaning the instrument and make sure the reference is not being pumped anymore. The reference can be turned off by unchecking Enable and Use Bottle A on the Ref Mass tab then clicking Apply Now and the Apply button.
When you're done for the day right click on the TOFMS icon group and select standby.
Finally analyze your data
Either click the View data button on the Sample run tab to launch Qualitative Analysis preloaded with the last analyzed sample or launch Qualitative Analysis from the desktop and open your data file manually.
On the lower left hand side there is a series of expandable windows. Open the one called Find Compounds by Formula if it is not already open. Click the first option Find by Formula - Options. This will open a dialog box
On the Formula Source tab enter in the formula for your compound by clicking on the radio button These formulas and entering your formula. Click the green play button near the top upper right hand side of the dialog box to search your TIC. If a match is found a new panel will appear on the screen showing the match information. Print this out by going to FIle --> Print --> Compound Report...