Manual Injector on Shimadzu HPLC system

Discussions about HPLC, CE, TLC, SFC, and other "liquid phase" separation techniques.

6 posts Page 1 of 1
Hello people,

I am trying to figure out how to properly use a manual injector on my new Shimadzu prep-HPLC system (Prominence). It’s one from Rheodyne and I just installed a 5mL loop but when wanting to start acquisition (so from LOAD I put it to INJECT) only the LC starts the underlying time program but neither the PDA are switched on nor does it record the separation.
So my question: How do I start an identical acquisition with the manual injector as with the autosampler?
I’m using LabSolutiobs as software btw.

Thx in advance!
Hi OddPain,

Whenever you turn the dial/valave from LOAD to INJECT, the method you currently have selected will run. This will not activate the PDA, will not save a data file normally, and will seem very strange. I've had this problem and simply work around it, but when you want to shoot an actual sample, here's my process:
First select and open the method that you want to run your acquisition on, follow that by clicking single run, naming your data file, and selecting a location for your data file to output to. Once you click start/okay, it will either bring up a pop-up window that should appear dead-center of your display that indicates start or cancel for the aforementioned run. At this point, you want to put your needle into the manual injector while in the LOAD position. Empty your syringe fully into the manual injector. Once you have loaded your sample onto the sample injector in the load position, turn the valve to the inject position with the syringe still in the manual injector. This opens the valve and allows your sample to be loaded onto the column, and not have your sample blasted back into your face like when I started using it. When it is switched to the inject position, the display on your screen should disappear (loading to injecting starts the run without having to click start), and you should have the PDA working as well as it has somewhere to direct the files to. This would be one proper run. While the needle is still in the injector, you can either pull it out (safe now), or leave it in for the rest of the run. I've seen arguments for both keeping the syringe within the injector, but if you're manually injecting on a 5 ml loop, I don't believe you'll see any differences depending on whether you leave it in or not.

As for an "identical" acquisition with the manual injector, I would say it is nearly impossible. Manual injection is simply more variable and depends on human error rather than the autosampler which, should be, relatively exact in all of it's measurements and injections. If you are asking how to start an acquisition using the autosampler, then I could help you better! First of all, in Lab Solutions you will want to navigate to the method editor and modify your favorite method to use the autosampler, which is as simple as going to the autosampler page in the method editor, clicking it on, and I would keep the standard settings regarding pretreatments, as well as the other numbers that come standard for now. After this, you should save this method file as a new method file, and probably place it in a folder that you will designate specifically for your autosampler methods. Now to actually use the autosampler, I always set up batches (because it's very rare, in my work, that I'm running a single run and I usually have 6-12 samples). In the method editor at the bottom of the screen next to your single run, you can click quick-batch to start making your batch queue. There are several things that you want to make sure about in this tab. All the method you use must be autosampler selected if you wish to use the autosampler-- even washes (I like to keep position 0 in the autosampler as my wash solution). From here you can set up your batch by selecting your methods, naming your samples, selecting injection volume, etc. I'm pretty sure there is a tutorial on youtube regarding batch queues that is pretty helpful as well. I'm trying to keep this as succinct as possible, so I know that I'm not being to specific, but if you run into a hiccup along the way, please don't be afraid to respond!
Unfortunately, however, whenever I use my manual injector, I find that my runs are never as precise as those of the autosampler. If you want to achieve better manual injector runs, I would suggest overloading the sample loop (roughly 3x the volume), in order to assure that your sample is tightly packed rather than dispersed before you switch the valve to injection. Ideally this should reduce your laminar flow as much as you can with an autosampler, but, obviously, you will still experience the effects of your large-volume sample slowing near the edge of your tubing/column due to these effects, but now it won't be multiple dispersed droplets that started at various spots on your injector due to the speed or force you used to inject the sample itself.

In my opinion, I focus mainly on prep LC, exact repetition is not the goal for my work. The goal I have is to purify as much of my target as possible, using the least amount of HPLC grade solvents. So my main focuses would be loadability of my compounds onto the column-- if I can expand the amount I can purify at once, then that's the direction I need to take. Or if I can include a recycling system (if using isocratic), and save X amount of solvent, that's the change that I will make. ALL of my peaks are somewhat overloaded, my retention times shift slightly but regularly, but I am still able to get pure products extracted in large amounts. Again, the goal of Prep LC is not to look pretty. Theoretical plates, constant retentions, etc. are NOT something I worry about. All that I care about is the resolution between my critical pairs and that my fraction collector is getting the right stuff. In this case, I would not worry too much about exact repetitiveness, but instead about your loading capacity and fraction collection settings. This also means that the differences between my manual injections and autosampler injections do not matter too much. Hopefully this helps in any way shape or form! Please don't hesitate if you would like me to elaborate on some of the LabSolutions settings or anything else.
Tyler Smith.
TylerSmith123 wrote:
Hi OddPain,

Whenever you turn the dial/valave from LOAD to INJECT, the method you currently have selected will run. This will not activate the PDA, will not save a data file normally, and will seem very strange. I've had this problem and simply work around it, but when you want to shoot an actual sample, here's my process:
First select and open the method that you want to run your acquisition on, follow that by clicking single run, naming your data file, and selecting a location for your data file to output to. Once you click start/okay, it will either bring up a pop-up window that should appear dead-center of your display that indicates start or cancel for the aforementioned run. At this point, you want to put your needle into the manual injector while in the LOAD position. Empty your syringe fully into the manual injector. Once you have loaded your sample onto the sample injector in the load position, turn the valve to the inject position with the syringe still in the manual injector. This opens the valve and allows your sample to be loaded onto the column, and not have your sample blasted back into your face like when I started using it. When it is switched to the inject position, the display on your screen should disappear (loading to injecting starts the run without having to click start), and you should have the PDA working as well as it has somewhere to direct the files to. This would be one proper run. While the needle is still in the injector, you can either pull it out (safe now), or leave it in for the rest of the run. I've seen arguments for both keeping the syringe within the injector, but if you're manually injecting on a 5 ml loop, I don't believe you'll see any differences depending on whether you leave it in or not.

As for an "identical" acquisition with the manual injector, I would say it is nearly impossible. Manual injection is simply more variable and depends on human error rather than the autosampler which, should be, relatively exact in all of it's measurements and injections. If you are asking how to start an acquisition using the autosampler, then I could help you better! First of all, in Lab Solutions you will want to navigate to the method editor and modify your favorite method to use the autosampler, which is as simple as going to the autosampler page in the method editor, clicking it on, and I would keep the standard settings regarding pretreatments, as well as the other numbers that come standard for now. After this, you should save this method file as a new method file, and probably place it in a folder that you will designate specifically for your autosampler methods. Now to actually use the autosampler, I always set up batches (because it's very rare, in my work, that I'm running a single run and I usually have 6-12 samples). In the method editor at the bottom of the screen next to your single run, you can click quick-batch to start making your batch queue. There are several things that you want to make sure about in this tab. All the method you use must be autosampler selected if you wish to use the autosampler-- even washes (I like to keep position 0 in the autosampler as my wash solution). From here you can set up your batch by selecting your methods, naming your samples, selecting injection volume, etc. I'm pretty sure there is a tutorial on youtube regarding batch queues that is pretty helpful as well. I'm trying to keep this as succinct as possible, so I know that I'm not being to specific, but if you run into a hiccup along the way, please don't be afraid to respond!
Unfortunately, however, whenever I use my manual injector, I find that my runs are never as precise as those of the autosampler. If you want to achieve better manual injector runs, I would suggest overloading the sample loop (roughly 3x the volume), in order to assure that your sample is tightly packed rather than dispersed before you switch the valve to injection. Ideally this should reduce your laminar flow as much as you can with an autosampler, but, obviously, you will still experience the effects of your large-volume sample slowing near the edge of your tubing/column due to these effects, but now it won't be multiple dispersed droplets that started at various spots on your injector due to the speed or force you used to inject the sample itself.

In my opinion, I focus mainly on prep LC, exact repetition is not the goal for my work. The goal I have is to purify as much of my target as possible, using the least amount of HPLC grade solvents. So my main focuses would be loadability of my compounds onto the column-- if I can expand the amount I can purify at once, then that's the direction I need to take. Or if I can include a recycling system (if using isocratic), and save X amount of solvent, that's the change that I will make. ALL of my peaks are somewhat overloaded, my retention times shift slightly but regularly, but I am still able to get pure products extracted in large amounts. Again, the goal of Prep LC is not to look pretty. Theoretical plates, constant retentions, etc. are NOT something I worry about. All that I care about is the resolution between my critical pairs and that my fraction collector is getting the right stuff. In this case, I would not worry too much about exact repetitiveness, but instead about your loading capacity and fraction collection settings. This also means that the differences between my manual injections and autosampler injections do not matter too much. Hopefully this helps in any way shape or form! Please don't hesitate if you would like me to elaborate on some of the LabSolutions settings or anything else.
Tyler Smith.


Ok thx very much. I will try this out!
One more question: would it be safe to use HBF4 in the HPLC? Or will it degrade the system? (Very little amount obviously)
Hi OddPain,

What would the use of the HBF4 be? Are you trying to use it as an acid as a mobile phase additive? I don't think I've ever heard of anyone using HBF4 as their acid component, and if you are attempting to use it as the acid component I would recommend something else. Since you're doing preparative work, which I assume implies you'll need to later on concentrate the samples or dry them, I would recommend Formic acid. Formic acid is perfectly safe for the HPLC, and has a significantly lower boiling point for lyophilizing/drying samples. If the acidic pH is all that you care about, then I would recommend phosphoric acid, although it is non-volatile if you plan on drying them. If you want something that can ion pair (somewhat), many chromatographers use triflouroacetic acid, and although I do not use it, many resources from manufacturers and journals use this add as their acidic mobile phase additive. If the HBF4 is in your sample, then I would expect everything to be fine, mayhaps reconsider your extraction techniques though. Good luck with your chromatography!
Tyler Smith
TylerSmith123 wrote:
Hi OddPain,

What would the use of the HBF4 be? Are you trying to use it as an acid as a mobile phase additive? I don't think I've ever heard of anyone using HBF4 as their acid component, and if you are attempting to use it as the acid component I would recommend something else. Since you're doing preparative work, which I assume implies you'll need to later on concentrate the samples or dry them, I would recommend Formic acid. Formic acid is perfectly safe for the HPLC, and has a significantly lower boiling point for lyophilizing/drying samples. If the acidic pH is all that you care about, then I would recommend phosphoric acid, although it is non-volatile if you plan on drying them. If you want something that can ion pair (somewhat), many chromatographers use triflouroacetic acid, and although I do not use it, many resources from manufacturers and journals use this add as their acidic mobile phase additive. If the HBF4 is in your sample, then I would expect everything to be fine, mayhaps reconsider your extraction techniques though. Good luck with your chromatography!
Tyler Smith


Thx again for the reply Tyler! I would want to use HBF4 as an additive in the mobile phase because I am separating a positively charged compound and using other acids will give me their deprotonated form as anion (I can see the formate anion in my sample) and I need a very weakly coordinating anion such as BF4 as well as staying consistent with my other substances I have that all use BF4.
Hi OddPain,

It seems like you are trying to use an ionic pairing selector with the BF4 being your anion, and your target being the cation. Please let me know if I have this assumption incorrect. When you say that your other substances are used with BF4, do you mean on that on the HPLC you have run them with this HBF4 modifier? If you have been exercising a method that you are simply upgrading to a preparative method, and you have seen no instances of degradation for your column or instrument, then I would say to keep using that as your mobile phase additive! Or does this imply that your other compounds are boron salts and you have been simply running those on a column? If not, like I mentioned before, many people use TFA as a similar, ionic pairing, additive. You can find countless examples of this reagent used with great success and may want to try it on your sample too. However, if you have evidence that the HBF4 has been working on a, lets say, analytical scale and you're simply "upgrading" your method to run on a prep LC, then keep doing what you're doing!

Also, if you give me some of your column specs I may be able to help more! The more information you give us, the more replies you'll get, and they'll be giving you better quality and more accurate information.

Anyway, good luck!
Tyler Smith
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