Orbitrap Users Daily Procedure

Before running the batch:

Create a new PF number for each new project, and a new PF number for each project at the start of the month. Supply an account number for each project to be billed at the end of the month.
Update the blue instrument logbooks daily. Put the PF number, lab and your name down. Use the Snippet tool to capture the sld information, then tape that into the log book. Use Windows Explorer Date Created and Date Modified to calculate the total acquisition run time and number of samples run and write this information down after the batch is done.
Check nitrogen gas levels on the tank. There should be at least 500 psi before starting any batch of samples. If you are unsure about the gas level, please ask the staff to check the tank.
Check that there is sufficient solvent in the NC pump A and B bottles, the loading pump A bottle and the wash solution bottle to last through the batch.
Before starting a set of runs, note the NC pressure at 5%B and 300 nl/min and the loading pump pressure at 4ul/min in the log book.
Run the 1 fmol and 50 fmol BSA standard every time you start a new batch to QC, record the score, % coverage, and retention times. BSA 1 fmol standard runs are not billed. If the BSA score is <10 or the RT shifted, then do not start samples. Look at peak width FWHM. I use peaks 653.36 2+ at ~15 min and 722 2+ ~13'. Normal peak width is 6-9 s.
Check that your transport vials and sample vials are in the correct position and have enough liquid for the batch.
In XCalibur, both MS (Orbitrap) and LC (Dionex) should show status as "Ready to Download". If not, right click and adjust status to on. See that the MS tune page shows on with green button, not yellow standby.

After the batch ends:

1) At the end of a batch, run the 1 and 50 fmol BSA standards and record information in the log book. Record the NC pump and loading pump pressures as in step 4 using take control on the Dionex home page to set the flow rate.

2a) Set up cleaning runs for when no samples are running. Do 10x cycles of wash/blank/IPA. This cleans trap and column with up and down gradients, blank gradients and isopropanol.

Alternatively, do 2b to clean column.

2b) Set the NC pump at 80%B, 300 nl/min, and the loading pump at 0.5 ul/min, then switch valve to 10_1 position This flushes trap and column with 80%B.