Spikes of column bleed

Those don't look like spikes, which have essentially no peak width, they look like chromatographic peaks. These peaks could be siloxanes from elsewhere, too. They show up from vial cap septa, injection port septa, solvent in plastic squeeze bottles used to clean the inlet or fill the ALS solvent rinse vials, etc.... anything plastic or silicone.  Use new ALS wash vials with solvent poured only from glass. Install a new syringe as that may be contaminated, too. 

Did you do full inlet maintenance along with replacing the column? What inlet - SSL or MMI? What liner is installed? Did you vent to replace ithe column and do the maintenance or did you replace it without venting?

Is this a MeOH solvent only injected run?  What happens with a no-inject run?  Do they get smaller with more no-inject runs?

The baseline is incredibly high. Two columns "connected with a PSD" -- using a purged ultimate union or a splitter to a second detector?  What is the exact physical column configuration - what columns, dimensions, phases, etc?  What is the software column configuration and flow/pressure setpoints on both?

Sorry, the peaks are chromatographic peaks of siloxanes. I wasn't sure the best way to describe them. The liner is a 5062-3587 splitless and the inlet is SSL. I replaced the liner and the septa but did no other maintenance on the inlet.

I did not vent to replace the column from the inlet.  I thought doing this was ok but question if that damaged the column on the MS side.  I let He flow over night before running samples, but the transfer line would have been heated.

I only have injected MeOH so far.  I'll try a no-inject run. The two columns are connected with a PSD.  The column on the inlet side is a 30m DB-5ms UI (122-5532UI) and the other is a 15m DB-5ms. I included a screenshot on column configuration.  Thanks for the help

If the transferline was hot and the MS sucked air in through it, that section is more than likely damaged. If the PSD pressure/flow was sufficient maybe not, but it probably wasn't high enough flow to ensure no air got in.  You can get away with it if you have a CFT plug fitting in your hand ready to go, remove the column, and quickly cap the Purged Ultimate Union.

The configuration above says that column 1 is 15 m and column 2 is 15 m....but you typed that column 1 is 30 meters...is that correct? If so, fix the column 1 configuration as that flow will be very wrong.  Column 2 should have the flow setpoint about 10 to 20 percent higher than column 1 -- or 0.15 to 0.2 ml/min higher.  So if column 1 is 1.0 ml/min, column 2 should be 1.15 to 1.2 ml/min.

Sorry, I uploaded a screen shot of the wrong method.  I attached the correct one now. 

Also, I started a no injection run and it appears that the peaks I was seeing before are gone.  The MeOH I was using was from a glass bottle but must not have been good.  I'm opening a new bottle and will run a blank with it and will replace the syringe also if needed. Thanks for you help.

If the siloxane peaks are in the liner or the front of the column you may need to perform inlet maintenance and cut 25 cm or so off the front of the column. 

There is another trick that might help remove those peaks.  Set the inlet to Split mode, set the inlet pressure to 1 or 2 psi, as low as it will control, and set the split flow to 500 ml/min gas saver off.  Using a syringe slowly hand inject a number of full syringes of known clean solvent, maybe eight or ten syringes full. Then reload your normal method to reset the pressures and flows and do a blank no-inject run.  I've had to do this twice a few times to reduce the peaks enough to continue running my tests.

They show up from vial cap septa, injection port septa, solvent in plastic squeeze bottles, plastic pipettes, solvent that has touched a pipette bulb, and more.