PhD thesis: How to mess shit up. #5- Damage capillary

Earlier this week.

Dr Eugene had low intensity in his infusion.

Dr Eugene: Phyliss... I was calibrating the mass spec and can’t get detector setup to pass. But yesterday, the intensity is ok, at e^4. Today it is e^3.

Me: Do you need to do it everyday?

Dr Eugene: No, but I did it anyway, it can’t pass.

Rolling my eyes. If you could get good intensity yesterday, it’s probably something you didn’t do it right today. Method parameters? I think it is unlikely that instrument will miraculously spoil today when yesterday worked well.

Me: I am not a TOF engineer, can you ask Dr Little Strawberry on your method setup.

Dr Eugene: Dr Strawberry.... could you help

It turned out that the lockspray capillary was bent. 

Dr Eugene: How could it become bent?

Do you even need to ask?! Obviously it must have hit something to become bent! The person who took it out or put it in had damaged it! 

Well I wasn’t expecting a damaged capillary problem because he said the instrument was working fine yesterday! And he did not do anything to the instrument, if you believe. So he took another ESI source, and intensity went up. Dr Little Strawberry also found that he used the wrong concentration, obviously would get 4 times lower result! He didn’t even check the calibration guide! But he passed the test without using the right concentration, and totally ignored Dr Strawberry.

Subsequently when I was replacing the lockspray capillary, I was going to show the scientists how to do it. I tried twice and it was ok, so I asked them to try it too. Dr Harmless Freesia did one round, and pass to Dr Eugene to try next. As soon as Dr Eugene touch it, it got stuck. No matter how hard he tried, I tried, Dr Harmless Freesia helped too, we all could not remove the probe tip!

I guess the o-ring could have been caught inside the screw threads. Probably from the uneven forces that they used to screw and unscrew. I really shouldn’t have let them try it! Urgh!

Well to be fair and I really don’t want to be, it could have been Dr Harmless Freesia, and may not have been Dr Eugene. But I find it really amusing, both the damages on the capillary, and the probe tip, happened when he touched them.

I used to tell my customers that I’ve got great magic hands. One touch and your problem would be resolved. It looks like Dr Eugene’s destroying powers were too strong for my magic hands to counter... 

I need to wake up my ideas and up my magic skills.

PhD thesis: How to mess shit up. #4- Pusher offset

I was working away from office until my laptop battery died at 4:30pm. Sadly couldn’t last the whole day. I thought of going back to office to wrap things up for the last hour.

Regret. It was a big mistake.

So Dr Eugene was having problem with tailing peak shape. He didn’t know how to tune it up, and neither do I.

Dr Eugene: Phyliss, could you come and have a look at the peak shape

It couldn’t have been a better timing. I just wanted to do something productive for the last hour! Reluctantly, I walked over.

Me: It is tailing...
Dr Eugene: Could you help to tune it up
Me: I haven’t tuned a TOF before. But I could try... based on my understanding of tuning the Quads.
Dr Eugene: Please, help. Can you do it now.
Me: I need to refer to the reference guide first. I need time to find the guide as well as to read and understand. It would be end of the day already, I’ll do it tomorrow.
Dr Eugene: Ok, go and read it now. 现在！现在！去！
Me: I said tomorrow.

I resumed the work I was meant to wrap up. Urgh, my work doesn’t revolve around you! I deliberately read other materials when he was around. Enough is enough! No more immediate help to this guy.

Then... Dr Little Strawberry came to the rescue. She’s been taught how to rectify this issue. The tailing problem was resolved by adjusting pusher offset. I wished it it had taken longer, so he could perhaps, find out the solution himself.

Next day, I was with Asst Service Manager (KR) to look for a driver. When he saw Dr Eugene, he asked, how’s this guy doing.
Me: Hmm.. Why are you asking about him...?
KR: He contacted me yesterday, to ask about a peak tailing problem
Me: What! He even contacted you? I didn’t know that... 😂
KR: He contacts me whenever DN is away.
Me: The peak shape problem was resolved by tuning the pusher offset. (Then I started my other complaints about him)
KR: Back when he was the customer, it was ok if he discussed over messaging. But he gets really panicky when he speaks on the phone, or when we are on site. If he uses an unknown number to call, I can’t avoid it...

I gave an understanding smile. I am astonished. It seemed like Dr Eugene has been desperately calling the whole world for help.

How did he even manage his PhD then?!

PhD thesis: How to mess shit up. #3- Wash tubing

Some time in early August. I was trying to avoid Dr Eugene because he had so many questions for me. I have a day job too and I need to get things done. Unfortunately we were in the same recreation committee and the team wanted a meeting over lunch.

Dr Eugene: Phyliss... I have something to consult you 

Me: Ok what..?

Dr Eugene: It’s the TOF, when I try to do an infusion, the signal keeps dropping... and then it was gone. 

Me: Ok... try purging...?

Dr Eugene: I have done it, many times. I have purged many times, but there was nothing. I even took out tubing by tubing to check. There was no flow. I suspect something is clogged in the tubing, I changed the whole probe. (I think he rebuilt the capillary). There was still nothing!

Me: The usual things to check.. purge more times, maybe there’s a block somewhere else, or it could be a leak. Trace the fluidic lines. Sometimes the leak is not obvious.... and previously it took me half an hour to find the leak when Dr Little Strawberry was having intensity problems. So usually these few reasons, purge, block, leak, and make sure the wash line needs to be submerged in the reservoir.

Dr Eugene: I have checked that too, the wash line is submerged in the solvent. 

Me: Ok... later we can have a look.

After lunch. I walked into the lab... And dang. Right away I could see the wash tubing was not in the solvent! It was hanging in the air. 🤦🏻‍♀️ And you said that you checked!!! You spent half an hour explaining the problem... and the whole morning to rectify.. it was due to this!

Me: Your wash tubing is not even submerged in the solvent!

Dr Eugene: Uh?! How could it be? I really had checked it just now!

Me: Ok ok... just purge and run an infusion now..

Dr Eugene: Ok, if you can stay for 15 mins, the symptoms will come and intensity will drop later. 

A while later..

Dr Eugene: See! See! The intensity is dropping!
Me: Ok then purge again and set a higher infusion rate.
.
.
.
The intensity never dropped afterwards.

Me: It’s ok now...
Dr Eugene: Let me take out the tubings again to check if there is a flow.
Me: Obviously there would be a flow since you can see signals in lockspray!
Dr Eugene: There is flow and signal now, but the signal is at e^3 (negative mode), it is low...
Me: So what is the usual intensity you get?
Dr Eugene: I don’t remember but this looks really low.

I changed to positive mode and it shot up to e^5. So intensity is high, and we know the flow is ok. You don’t have anything to compare against but say the signal is low? 👊🏻

Me: The flow is ok, check your standards again.

He was in denial... he could not accept that it was just due to wash tubing.

I can’t accept too. Wasting one whole day just because the wash tubing was not submerged in the solvent!!! What a waste of my time.

PhD thesis: How to mess shit up. #2- Cable

Lesson 2 - Check your cables...

Earlier this week... Dr Eugene changed the source of mass spec as he took over the instrument from another scientist.

Dr Eugene: Phyliss, the software does not detect the source. Usually clicking at ‘source’ would show a drop down menu of ionisation modes. It is not showing anything now...
Me: Er... I am not familiar with TOF you know... try to restart software?
Dr Eugene: I have done it, many times. Even restarting the computer, it just doesn’t work.
Me: Restart instrument electronics then?
Dr Eugene: I don’t know how to do it, let’s ask Dr Little Strawberry.
Me: No no we don’t need to ask her. I know this very well (same across all MS), it’s very intuitive. Just look at the 2 switches, one says ‘pump override on/off’ and other says ‘electronics on/off’. You want to switch to ‘pump override’ before turning off electronics. Because without pump override, turning off the electronics will turn off the pump, instrument will vent.
Dr Eugene: So this is to protect the pump
Me: No, (obviously no!) this is to keep the mass spec in vacuum state so you don’t have to wait half a day before you can run samples. Instrument takes a few hours to pump down...
Dr Eugene: Ok I get it.
Me: You don’t want to switch off ‘pump override’ before turning on electronics, otherwise the pump will switch off and instrument will vent, electronics turn on. So electronics on, then pump override off.

Restarting the electronics didn’t fix the problem. Then, I thought... since the software couldn’t show the ionisation modes, it probably is not detecting the source? 🤔 Reconnect cables...

When opening the cover, true enough the yellow cable was not pushed all the way! Pushed it in and the software shows the ionisation modes right away. 🤷🏻‍♀️

This reminds me of primary school exams. Mistakes you made, not because you didn’t know how to do it, but because you didn’t check your work. Carelessness.

1 hour later.

Dr Eugene: I am reading up some slides about the instrument. It says that there are 2 ways of restarting electronics, one from the front and one from the back. Could you show me how to do it from the front?
Me: There is no button on the front of the instrument so you can’t do it from the front. It’s just how this instrument is designed.
Dr Eugene: Ok, what does the pilot valve mean then?
Me: I am not a TOF engineer and I am not sure. It’s the valve on the bottle trap to shut off and on for source pressure test, I think. Read the operators guide and you may be able to find the explanations there. (I am not your Google!!!)
Dr Eugene: I don’t remember my previous company has a bottle trap for the mass spec...
Me: All our company’s mass spec comes with a bottle trap. You probably did not notice it before because it is behind the instrument.

Come on... You book the instrument but use the time to read about TOF parts? Run your important samples first before you find other time to read! Priorities!

PhD thesis: How to mess shit up. #1- Set probe temp to 0

Is common sense not so common after all? The amount of stupidity I get from people triggers me. I can’t fathom how someone with no common sense can be given a PhD!!

I used to be very much in awe by people with PhD, at least the lab where I came from - there were President scholar, Harvard graduate, ASEAN scholar... you name it. Sometimes it demotivates me, because I will never reach that level. On the good side, their thought processes inspire me. To think further, think deeper. How to carry myself. Be more composed.

So my encounter with this guy amuses me. Let’s call him Dr Eugene. A Dr title because he has a real PhD ok!

So yesterday... 

Dr Eugene: Sorry uh Phyliss. Could you come in to have a look (at the mass spec instrument).

Me: Ok...

Dr Eugene: I saw that the Ar gas was empty (regulator points to 0psi), so I turned it up. Now it says ‘collision cell overpressure’. The software shows the collision cell pressure e-2, but I have recorded down previous readings, it should be e-3.

Me: Ok... so you turned up the Ar gas. It reads 30 psi now, what should the value be?

Dr Eugene: Uh.. I don’t know

Me: Ok.. That’s ok. We can find out from the installation guide. I’ll check on that.

Reading installation guide... it says.. Argon gas should be regulated at 7.25psi, dang! 🤦🏻‍♀️ That’s why the original reading was correct! Don’t create someone out of nothing!

The scale of the regulator was rather wide, maybe 0-200 psi. That’s why 7psi would look like there is no gas! Why would you even turn it up when you don’t check the guides how much to do it! 

Based on feeling huh, apparently,

So I closed the valve, but it doesn’t release the Ar gas. 

So I suggested: Why don’t you set some MRM injections to exhaust the Argon gas, while we keep the valve close. Or running infusion and do some fragmentation.

Dr Eugene: But we can’t even change the tune page settings! Look, in standby mode the voltages are switched off and at 0!

He then demonstrated, probe temperature was set at 300 deg C. If he changed the the probe temperature setting to 0, the software would not respond and jumps back to 300! 🤦🏻‍♀️🤦🏻‍♀️

Do you really think the probe is capable of achieving 0 deg!!! Have you ever seen the probe freezes up!! (It’s like buying a kitchen oven, with futile attempt to set it to 0 deg.)

Me (Breathes): Why don’t you set a higher temperature like 50 or 100.

Dr Eugene presses 50 and hit enter. It worked...

Now, run your injections and exhaust the Argon gas. 

He went on to explain how he doesn’t want to do it over the weekend because he doesn’t want anything to go wrong, and nobody would be around.

I don’t care when you do it. 

So there was nothing wrong with the instrument! The instrument is innocent! Stop blaming the instrument! 

Even better, stop touching it!

I am not even a full mass spec engineer. I may have attended an Engineers training 2 years ago, sadly never had the chance to work on it. I am unfamiliar with HRMS. But it doesn’t take a mass spec engineer to recognise the problem. You just need common sense.

Highlight of the day.