Bio-Rad Ciphergen PBS-II back to life

That’s a mouthful, but it’s an instrument, for science and stuff. I got a used one from eBay last week, and finally have it set up to where I can actually talk to it over the crude computer interface, it’s been a fun process. I’ll back up: this thing is an analytical instrument from the early 2000s. It is designed to measure the distribution of mass in a sample (such as as a sample of proteins from tissue cells). It does this by blasting the sample with a pulsed UV laser (337 nm, nitrogen), accelerating the charged particles (ions) across a high voltage, and measuring the time it takes them to reach an ion detector a few feet away. The distribution of arrival times is therefore a distribution of charge-mass ratios (a spectrum).

Long story short, it has a whole lot of good physics equipment in it, even if it doesn’t do it’s biology thing very well anymore (though it might…  I don’t have a good sample to test it on). I bought it for the parts, and want to see what it can do. This is an outline of the steps I took to get it working. While it may not apply to anyone else, the tricks are generally useful for hacking on vintage instruments.

This machine originally came with a PC for control, and it communicates via GPIB port. This is not always my favorite platform to work with, but it is here to stay (at least it was in 2000).

I have a prologix USB-GPIB so my first try was to set that up with the machine. It took a while (and a few passes through the manuals) to find the note that the PBSii defaults to address 8. Once that was set correctly, it responded to *idn? with Stanford Research Systems,TOF200,ver045 which was a bit surprising. It turns out SRS was working on a time-of-flight mass spectrometer (similar to this) at that time, and must have been selling time-of-flight boards for OEM use. I pulled out the TOF board to take a look, and noticed that it connects to the master box via a cable labeled “SPI”. Despite being an actual protocol, I think this refers to “Serial Port Interface” as the manual has that phrase in a few locations (but no real information beyond the name). There are a few GPIB commands listed in the service manual, things like how to read and set various registers, but nothing very high-level (the design relies on the software for all of that). I didn’t try those commands right away because without knowing what they did… I’d risk setting the machine into some odd state or enabling a subsystem that I shouldn’t.


The SRS time-of-flight controller embedded in this instrument. GPIB chip (NAT9914) hiding under the top left ribbon cable.

Talking over GPIB was encouraging, but I still had no control over the vacuum system (or any readings from the gauges and various system status indicators). When it powers on, I could hear valves snapping open (or shut) and the pumps would start up; it clearly had a turn-on sequence and everything at least appeared to be working at this point.

After a few emails to the company, including an initial response to the effect of “that machine has been unsupported for over a decade,” I was sent a zip of the original software utilities. Lesson 1: the sooner you can get to an engineer in the company, the better. Find someone like you who enjoys diving in and isn’t afraid of the hardware-software boundary. Unfortunately, the software didn’t see my USB interface as a GPIB (why would it, its just a serial port). I couldn’t yet use the utility software. Sure, there may be some way to trick it into sending GPIB to the serial port, but a more direct route would be to revive some appropriate-era hardware.

The next step was to track down a PC with a GPIB card capable of running the windows utilities. They were written for Win2000 so I figured anything from NT to XP should work… and maybe even later. I borrowed a dusty XP machine from a colleague’s lab for some debugging. In that era of windows, there is an option for “Remote Desktop” which is nice, so I can check on things from outside the lab. Lesson 2: if you don’t want to be stuck in the same room as the machine for a week, set up VNC, remote desktop, or some other way to remotely check in on it

Fortunately everything fired up without a hitch, and the utility software started reporting status and accepting commands. At first, it reported the MAG gauge (high-vacuum gauge) at 0 volts, and turbo pump speed as LOW. Additionally, the backing valve was showing OPEN even though all valves were listed as commanded CLOSED. This was concerning, but not surprising given that it’s probably been sitting for at least a couple years. I cycled the power and the next time around both gauges were alive, and the turbo pump spun up to report OK. In retrospect, I should have followed the shutdown routine to make sure valves were properly closed and the turbopump was allowed to spin down before anything was vented. It seems to have defaulted ok, and the turbopump took a long (quiet) time to spin down. A good sign given the fact that turbos can be seriously damaged if vented too quickly.

Screen Shot 2018-10-21 at 12.18.58 PM

A screenshot of the utility software reporting the current status.

Now I’m at the hurry-up-and-wait stage of pumping down to 1e-6 Torr at which point I can fire up the high voltage and laser systems. I’ve only worked with a handful of vacuum systems (back in grad school) but I did remember that it’s useful to have a reference pumpdown curve… so I started charting away. This is where Remote Desktop really helps. I’d log in every so often to peek at the reported pressure. After 12 hours, it’s gone from roughing to 5e-6 Torr. The operating target is 1e-6, so we still have a ways to go. The flight tube had been open to atmosphere for who knows how long, so I suspect a bake-out is in order, and likely a replacement seal or two (rubber o-rings have a limited lifespan, especially in surplus storage warehouses).

Overall, it’s pretty cool to have something like this come to life even just to this level. At the very least, I got an operational high-vacuum system for $750 plus freight. Lesson 3: a lot of instrumentation is built from generally-useful parts. Such instruments become useless to the intended users even if only one tiny part stops working. Even worse, they become obsolete only through lack of software support. eBay is your friend, but you may have to battle your business office… mine requires personal payment and will only reimburse after equipment arrives on campus.

I owe a shout-out to Erik Sanchez from PSU who tipped me off on this amazing used-equipment find and sent me many helpful documents. Also thanks to Windell Oskay for a helpful conversation as I was starting out. He spent time as a hardware engineer at SRS, and gave me some insight on their hardware implementation of GPIB (using the NAT9914 chip).

Update: After about 48 hours, it wasn’t going below 3e-6 Torr so I started through the various seals and valves. There are several, all too specific to worry about here, but I cleaned the main sample seal o-ring with isopropyl alcohol, and cleaned out the two valves that vent the flight tube to higher pressures (one to atmosphere, one to the backing pressure). At this point, 12-hours later, it’s down to 1.2e-6 (closer!). I’ll give it a day, and see how it looks. Bottom line, the turbopump seems to be in working order (knock on wood) despite me absent-mindedly venting to atmosphere for a few seconds (doh!).

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