Chromatography Forum

Hi everyone,
i am looking for information on these systems. Can anyone shed some light? I want to buy one system next year as my first and wanted to know more about them or if you have run side by side comparison.
if you have can you share the data with me so I can then contact my sales person to do a demo and really do a side by side comparison. I have read from Ken already, but I think Ken is so fixed on ABI it is completely biased or maybe Ken is really a sales person from ABI. I see that he shared no new information that is already know to the public. Also the claim that it is 50x more on some compounds is totally bull. Unless they have data showing this then i dont believe it.
I hear that the Vantage can already go down to fgram levels.
so what Ken is saying here is that the 5500 can go down to agram levels?
that is a lot of *(&)(*
actually wait... this is possible if they are doing nanospray. i then can believe it however, i think that every system can go down to agram levels with nanospray.
i want to see the real real data not just sales pitches.

so if you actually have head to head data show it!

{Also the claim that it is 50x more on some compounds is totally bull]

I have to agree with you on that

Hi Cy and all, just want to make things simple and to clarify certain doubts.

i) Firstly, I am not an ABI sales guy. ^^

ii) I might sounds like I am pro-ABI - this is because I am/have used ABI, Waters and Agilent systems before and I am really fond of the ABI systems because of performance criteria.

iii) ABI 5500 can go up to 50X on certain compounds; I am not saying all compounds but some compounds - this was presented to me by the ABI experts; so I dont think its all 'bull' as they have shown me some data on the system performance.

iv) 2 weeks ago, they made a side by side comparison with Thermo Vantage and found that ABI 5500 is 10X better in term of sensitivity; though I have yet to see any real data from them ; I will request them to send me the data soon for me to evaluate.

v) Cy, I can see that you're trying to make evaluation for a system purchase which is completely justifiable; I am just curious why do you want more data etc from us here before contacting your sales person for a demo to be done?

As for me, I have always requested demo to be conducted before making any decisions; so, why dont you just go ahead and make a request to all vendors interested for a demo to be done so that you can make your decision based on which system performs the best? Rather than asking us over here; I guess the best choice for you is to have a demo run; then you will be able to have concrete information at first hand, right?

Cheers !!!

P/S: Hope I can get my 5500 before year end or early next year ^^

So what is the 50x on compounds? is it against there own systems or other vendors?
only 10x vs Thermo's Vantage? was that on a actual compound or was it on reserpine? I dont care much for reserpine data. was it in neat that they show you this 50x or was it in matrix?
I am interested to see some data so i can see also. I have requested a demo with Thermo, ABI, Agilent as well as Waters.
running 600 pesticides with 2 daughter ions so a total of 1200 transitions.
i want to see how low ever vendor can go.
but it will be in avacado extract! not this neat stuff. any vendor can do well in neat but i want to see what they can do with avacado.

If you have data share it I would like to see. I will post all of my results after I finish all of my demos.

Hey Cy, our lab recently received demo data following testing of 18 AQUA peptides for targeted quantitative proteomic applications in our lab. In these demos, the ABI 5500 QTRAP, Thermo Vantage, Waters Xevo and Agilent 6460 were compared and we found that the ABI 5500 was about five fold more sensitive than any of the other platforms. Furthermore, our samples were initially run on an ABI 4000 QTRAP in comparison with the other vendors and it was more sensitive than the Xevo and 6460. The one major disadvantage of the ABI instrument is that the mass range is only 1-1000 m/z. While most likely will not be an issue for small molecule work, one important thing to keep in mind is that if you decide to monitor peptides or proteins later on, the mass range limit could be a factor.

Hi dh,
thanks for that information. one of our main quant will be in pesticides however we would like to see peptides also and i realize that the 5500 m/z only goes to 1000 which might be a limiting factor for me. which means that ABI is using either the +4 or +5

do you think you can send me a data packet with the results? what about the Thermo system? You did not mention anything about them.
I will be sending out pesticides like I said earlier, but in light of the low m/z range we will be also sending in 100 peptides. I have given them 2 weeks to complete the data and i will visit them and see the system.
interesting to see that the ABI system is the same size as the Thermo system as well as the color? I wonder why they are doing that? maybe to confuse the customers?

All the dilutions will be made in house as a big batch and send out to all vendors. will be running these same samples at my friends company and get the quant data so we know exactly what the data should be.

i have heard some vendors cheat and claim they can not see what the customer dilutions and has to make their own. which i have heard from 2 vendors now.j

all vendors has to show all of my pesticides down to 1ppt with 50ul injected. the peptide needs to be as low as they can get it.
I will be providing only 50ul of the samples with dilutions down to 1ppt also.
How far down did the vendors show you?
if you can send me the data i would greatly appreciated therefore, i can make adjustments.

How do you know that the data at your friends lab will be a reasonable standard?

they are mass spec specialist. they have about 20 MS/MS system from all the vendors. I think I can trust them. they are also a CRO so they have SOPs they have to follow so I can think I can trust him. That is the only kind of lab i will go to.

In terms of the mass range (1-1000 m/z), ABI looked at the proteomics literature and found out that in > 95% of the cases people using transitions with <1000 m/z for tryptic peptides, and that was the reason that they used that specification. That makes most people working in protemics skeptical. If they had allowed the mass range to go up to 1200 /1400 or they have kept the 1000 m/z units but allowing an option where you can monitor from 400-1400 they would had alleviated the problem. Limiting the mass range provides some benefits (in Thermo's case has to do with their newly introduced S-lens).

Furthermore, I think that for a good comparison you need to specify the chromatographic conditions, including column, length of gradient, mobile phase to be used etc (I would go as far as to provide them with the column that I want them to use), otherwise sometimes you are just comparing how good the application chemist is in each company. I would make sure to make clear at least the internal diameter of the column. You might also want to specify number of segments to be used and maybe dwell times (one of ABI's strength is that they can go down to 2 msec dwell time and 3 msec of pause (interscan) time, making a total of 5 msec per transition which helps with mutlicomponent analysis).

Also, when you are asking for a mixture of peptides to be analyzed where the majority of them will probably be multicharged you should clarify to Thermo that they can not use their FAIMS device (unless you are thinking of buying it). By applying the appropriate compensation voltage you can eliminate all single charged ions from entering the mass spectrometer, significantly improving the S/N.

Finally, for one study that I am aware that had to do with the use of peptides and nanoLC, only Waters Xevo was able to identify all the spiked peptides (which might had to do with the use of UPLC). I was told that all tandem mass spectrometers performed at about the same level in terms of sensitivity within 2x. One of the manufacturers didn't stick in the specifications requested (i.e. 1 hour gradient and did all experiments with 30 min gradient). All major manufacturers were tested except from Agilent.

Hi kostas,
thanks for that... i have sent each vendor the same column which i already have ran the pesticides as well as the peptides on. it is a simple column with simple HPLC methods. Nothing fancy.
all peptides to be a run of about 80mins while the pesticides within 30mins with pos/neg switch. NO Timed or Scheduled SRM or MRM (depending on vendor). The way it works out is that about 90-95% of the pesticides will come out very close to each other with a possiblity to have cross talk... ah yes i made sure that each vendor will be able to show cross talk.
I want a dwell time of 1sec with no Scheduled SRMs/MRMs (same stupid thing). Min. requirement scans under peak is 10 no less. they will have to show the TICs under the scan for each calibration curve.

I dont care about this FAIMS thing... waste too much gases which my company can not afford.

This will be a full test to see capabilities of their system. I dont care about the QTrap part of it useless.

this is full quant with all the needed specs for my company.
robustness is another assay they will be doing.

each vendor has a eactracted solution of ginger and avacado.
they will need to show me 400 injections at 2ul at 1ppb and 0.5ppb with the spiked pesticides.

dont worry the apps chemist is not being tested here because all the methods have been certfied to work. all the possible LC conditions from Agilent to Thermo to Waters are provided. they have to use the same conditions as well as the column and mobile phases.

Optimization is up to them. since it is a mixture of tons of pesticides good luck.
it is also stated in the demo that they use default parameters on their MS/MS. I will not have time to optimize each analyte so... who ever can show they can use their system without optimization will win bonus pts.

i realize that most customer are smart and some just go by what the vendor tells them to do. I had an Agilent person tell me to run just a few compounds on their 6460 as well as ABI. Only Thermo and Waters said bring in anything. So i give them everything to each vendor.

I will see how well each system performs and not the chemist. I have told the sales rep for each company that already.

I expected either really good results or just really bad results.

and yes... no tuning solution. highest concentration i have is at 50ppb and lowest is at 1ppt. i think most system can not tune in full scan at this level only good at srm/mrm mode.

CY2008,

If you have really provided these specifications, you have asked for an impossible task. There is no way in earth that you can achieve 10 points per chromatographic peak with 1200 transitions, no scheduled SRM's and 1 sec of dwell time. By enforcing 1 sec of dwell time (I ignore interscan time as it will be insignificant in this example) you will need around 1200 sec per cycle time (i.e. the time it will take to scan all transitions once). If you want 10 points per chromatographic peak you will need to have peaks that are 12000 second long which equals to 200 minutes chromatographic peaks, an impossible task...

Hi kostas,
thanks for that... i have sent each vendor the same column which i already have ran the pesticides as well as the peptides on. it is a simple column with simple HPLC methods. Nothing fancy.
all peptides to be a run of about 80mins while the pesticides within 30mins with pos/neg switch. NO Timed or Scheduled SRM or MRM (depending on vendor). The way it works out is that about 90-95% of the pesticides will come out very close to each other with a possiblity to have cross talk... ah yes i made sure that each vendor will be able to show cross talk.
I want a dwell time of 1sec with no Scheduled SRMs/MRMs (same stupid thing). Min. requirement scans under peak is 10 no less. they will have to show the TICs under the scan for each calibration curve.

I dont care about this FAIMS thing... waste too much gases which my company can not afford.

This will be a full test to see capabilities of their system. I dont care about the QTrap part of it useless.

this is full quant with all the needed specs for my company.
robustness is another assay they will be doing.

each vendor has a eactracted solution of ginger and avacado.
they will need to show me 400 injections at 2ul at 1ppb and 0.5ppb with the spiked pesticides.

dont worry the apps chemist is not being tested here because all the methods have been certfied to work. all the possible LC conditions from Agilent to Thermo to Waters are provided. they have to use the same conditions as well as the column and mobile phases.

Optimization is up to them. since it is a mixture of tons of pesticides good luck.
it is also stated in the demo that they use default parameters on their MS/MS. I will not have time to optimize each analyte so... who ever can show they can use their system without optimization will win bonus pts.

i realize that most customer are smart and some just go by what the vendor tells them to do. I had an Agilent person tell me to run just a few compounds on their 6460 as well as ABI. Only Thermo and Waters said bring in anything. So i give them everything to each vendor.

I will see how well each system performs and not the chemist. I have told the sales rep for each company that already.

I expected either really good results or just really bad results.

and yes... no tuning solution. highest concentration i have is at 50ppb and lowest is at 1ppt. i think most system can not tune in full scan at this level only good at srm/mrm mode.

i want to see what the system and software can do... also the peaks are going to be wide enough for them to do this experiment. trust me this experiment they can not fail with the chorom i have done.
each peak will be significantly wide enough for this esperiement to work.
we now have ran this one 3 systems here at my friends CRO and it is nice.

remember there is no Uhplc here all normal chromo.

this is real world situation. we have to monitor a lot of pesticides/pcpp/antiobiocs/steriods etc with IS. so I dont feel why these vendor who push their system with say >2000 srms/mrms cant do what i ask? if it is all scheduled srm/mrm they are doing then that is a shame because almost every vendor can do this.

they have a task to show me. I have not been running scheduled here at my friends CRO and it is ok... i think we have about 5 scans to 9 so whats the big deal?

cycle time/cycle time... its all about cycle time... we might go to a trap for this also...

but we want to see what each vendor can do... i have proposed bonus pts in this demo.

Thermo has agreed to do it and so has agilent and waters... i still havent heard from ABI.

of course i dont expect them to have all the data so let see what they can do to show case their instruments.
I had Thermo do pos/neg with their Access system with 330 srm's 150 pos the rest in neg.
they had about 9 scans w/o scheduled or timed srm/mrm

so why not with the newer system?

I am with Kostas on the 1200 MRM issue.

I have been working on pesticides for quite a while, 1 ppt in pure solution and direct injection is very difficult for any MS. Be reasonable, the strictest country-wide regulation for pesticide residue is 0.01ppm for foods and 0.1ppb for water.

They have 2 ways of doing this... the first is to show me everything in one scan event the bonus is to show me the difference if they do schedule or timed srms/mrm

our company thinks that the detection limit should be lower by our standards. this is going to be in matrix and not neat solution. So i think i am being fair to the vendors. everyone likes to run neat... I dont care for neat it is useless if you ask me.

Actually the scan is not 1 sec it is 0.001s this is what they have to run with.

ABI has introduced MRM3 in thier 5500 Trap system when compared with other vendors like Thermo,Agilent and Waters and I strongly beleive this is an added advantage while you are doing pesticide quantitation.

And being of user of Agilent , waters and ABI I can say that we are very happy with ABI's performance in our lab and our comfortable level is high with their system.

Why dont you look at thier new application note wherein you can analyze 1000 pestcides in a single run!.

The limited mass range is not an issue of the system as I never saw any pesticide crossing 1000 da and when you use for peptides also it is not going be an issue as it gives multiple charged species.By using deconvolution software you can break them into singly charged species and can identify.

Please check with waters sales person that why did they use sulfadimethoxine for determining MRM sensitivity instead of regular reserpine.