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Help interpreting Mass Spectra - Any experts with mass library access or analytical experience? Options
 
endlessness
#1 Posted : 12/4/2011 12:26:52 PM

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Hello,

I am looking for members who have access to mass spectra libraries and/or have experience in general analysing plant extracts and can help me out interpreting the results, identifying the peaks from GC-MS (EI), and in the future HPLC-MS (ESI).

I have the file in .MS format, which is the raw file from agilent. They can be opened with AMDIS software to check the peaks ( The free libraries offered in AMDIS and NIST 08 demo are very limited).

Otherwise I can also print PDF files with the spectra.

The peaks will be anything that is typically present in ethnobotanical plants: alkaloids, phenolic compounds, fatty acids, etc. Also impurities from extraction/solvents, as potential phthalates, etc.

Im very new with this analytical chemistry so I dont already know at first glance how to identify what compound it is or at least what kind of class of chemicals it is (unless its like DMT or a couple other tryptamines), with time and experience im certain it will be quicker. I am able to identify some compounds, but many not.....

If you think you can help me out, please voice here or send me a pm, I already have some plant extracts of interest to the community that I need help with. Thanks!
 

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Vodsel
#2 Posted : 12/4/2011 12:37:57 PM

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It's not my field at all, but I can offer Mass Spectrometry - Instrumentation, Interpretation and Applications ( 2008 ), and Time-of-Flight Mass Spectrometry: Instrumentation and Applications in Biological Research ( 1997 ). Maybe others, let me know if they can be handy Smile
 
Mindlusion
#3 Posted : 12/4/2011 1:46:45 PM

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I have a few good spectra libraries saved here, your looking specifically for tryptamines?

Can you send me your data? PDF would be nice, but i can get AMDIS no problem
Expect nothing, Receive everything.
"Experiment and extrapolation is the only means the organic chemists (humans) currrently have - in contrast to "God" (and possibly R. B. Woodward). "
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benzyme
#4 Posted : 12/4/2011 2:41:31 PM

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hey endlessness,
I tried opening the prog with WINE, but for some reason it won't open the spectral viewer (only the file window loads).
if you could take screenshots of the spectra, I'll certainly take a look at them.
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endlessness
#5 Posted : 12/4/2011 3:47:41 PM

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Yeah benz I couldnt open with WINE either, I had to go to windows dual boot to open the AMDIS properly.

Mindlusion, I suggest you get AMDIS, its the best way to explore the data properly

Im attaching phalaris AQ1 and phalaris yugo red .MS file. Im pretty busy but I made screenshots of the different peaks of AQ1 (for some reason I cant get the print option to work in this program, it doesnt print all peaks, just some random ones? ) . If anybody can get to print/export the mass spectra of each individual peak or feels like opening with AMDIS and screenshooting each peak of yugo red, for benz to help us, please do.

What I have identified so far:


AQ1


1.6318 - (Intgr 28552) Likely 4H-Pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl- , probably decomposition product from amino acids/plant sugars (http://pubs.acs.org/doi/abs/10.1021/jf00041a006). Mass spectra certain vs uncertain peaks
1.7124 - (Intgr 72757) Unknown. Mass spectra certain vs uncertain peaks
2.006 - (Intgr 20668 ) Coumaran ? (Natural Plant antifeedant against insects). Mass spectra certain vs uncertain peaks
2.185 - (Intgr 33209) - Benzeneacetic acid ? Mass spectra certain vs uncertain peaks
2.313 - (Intgr 33750) - Benzoic acid, 3-methyl- ? Mass spectra certain vs uncertain peaks
2.493 - (Intgr 19157) - Indole or some simple indole substance. Mass spectra certain vs uncertain peaks
3.0640 - (Intgr 381853) Some carboxylic acid - Mass spectra certain vs uncertain peaks
3.520 - (Intgr 11186) - 7-Methoxyindole or another similar substituted indole ? - Mass spectra certain vs uncertain peaks
3.615 - (Intgr. Signal 21029) Likely traces of Hordenine or another phenol-based substance . Too weak signal to identify but similar retention time to "clearer" hordenine match in yugo red at 3.54. Mass spectra uncertain peaks (certain only base peak 58 )
4.6598 - (intgr 17442) Unknown. Mass spectra certain vs uncertain peaks
5.463 - (Intgr 65750) Unknown. Mass spectra certain vs uncertain peaks
5.5223 - (intgr signal 117496) DMT
5.5906 - (intgr signal 5271, Traces, unknown, some dipeptide?) Mass spectra certain vs uncertain peaks
5.687 - (intgr signal 15066) - Unknown. Possibly some naturally present alcohol? Mass spectra certain vs uncertain peaks
5.7199 - (Intgr 38956) Possibly some naturally present ketone. Mass spectra certain vs uncertain peaks
5.7854 - (Intgr Signal 24802) mistery substance. The spectrum with certain peaks, vs spectrum with uncertain peaks, seems similar to caffeine, but caffeine shouldnt be there in phalaris. Caffeine has molecular weight 194, which should be the molecular ion but if you put the unsure peaks, there are some peaks of 300+m/z. And you can see the MW estimates go off if you add the uncertain peaks so I dont know what to say.
5.8664 - Phthalate (contamination from plastic used at some point during extraction) Mass spectra certain vs uncertain peaks
6.143 - (Intgr 11984) Fatty acid. Similar to some kind of decanoic acid, like Dodecanoic acid, 2-methyl- ..
6.207 - (Intgr 8893) Possibly 2MTHBC but weak signal and seems like too heavy molecular ion peak at 271. Mass spectra certain vs uncertain peaks
6.334 - (Intgr 329262) Very likely n-Hexadecanoic acid (Palmitic acid), very common fatty acid. Mass Spectra.
7.0313 - (Intgr signal 105603) Phytol, present in chlorophyll. Mass specra certain vs uncertain peaks
7.1348 - (Intgr 31076) Unknown. Mass spectra certain vs uncertain peaks
7.219 - (Intgr 210097) - Probably some carboxylic acid. Mass spectra certain vs uncertain peaks
7.224 - (Intgr signal 386362) - Probably some carboxylic acid. Mass spectra certain vs uncertain peaks
7.5855 - (Intgr signal 65204) Unknown, probably some plant alcohol. Mass spectra certain vs uncertain peaks.
8.2438 - (Intgr signal 144019) oleamide
8.7435 - (Intgr signal 4816) Unknown trace substance, weak signal.
10.1317 - (Intgr signal 10302) Unknown trace substance
10.3721 - (intgr signal 813115) - Some long chain unknown compound. Very possibly some fatty acid. Mass spectra certain peaks and uncertain peaks
11.9322 - (Intgr signal 76516) Plant cholesterol
12.1106 - (intgr signal 116904) Plant sterol. Mass spectra certain peaks vs uncertain peaks
12.4669 - (Intgr signal 302283) Plant sterol.
12.5754 - (Intgr signal 13693) Plant sterol
12.7453 - (Intgr signal 3607 Unknown trace component)


Yugo red:


2.498 min - Some indolic compound?
2.615 min - Some phenolic compound?
3.0635 - Another fatty acid ?
3.5435 - Possibly Hordenine or another phenol-based substance (Intgr. Signal 727484) 1- Mass spectra of "sure peaks", 2- Mass spectra with unsure peaks + MW estimation
4.5216 - Similar to gramine, some analogue?
4.7401 min - Gramine
5.5183 - DMT
5.6874 - Possibly some naturally present alcohol?
5.7808 - Unknown. (Intgr Signal 72181), and the certain vs uncertain spectrum seems similar to caffeine, but caffeine shouldnt be there in phalaris. Caffeine has molecular weight 194, which should be the molecular ion but if you put the unsure peaks, there are some peaks of 300+m/z. And you can see the MW estimates go off if you add the uncertain peaks so I dont know what to say.
5.867 - Some kind of phthalate, impurity from plastic used in extraction
6.1435 - Fatty acid
6.3380 - (Intgr. Signal 282044)- VERY likely n-Hexadecanoic acid (Palmitic acid), very common fatty acid. Mass Spectra
7.0929 - (Intgr signal 282605) Phytol, substance contained within chlorophyl. Mass spectra
7.219 - Some carboxylic acid
7.2441 - Some carboxylic acid
8.2 - oleamide - I heard it was found leeching from PP plastic, or you think naturally present in phalaris?
10.37 - Some long chain unknown compound. Very possibly some fatty acid.
11.9292 - (Intgr signal 51866) Plant sterol
12.1156 - (Intgr signal 25069) Plant sterol
12.4642 - (Intgr signal 244291) Plant sterol


Big Medicine:



3.556 - (Intgr signal 106860) Very likely hordenine
5.52 - (Intgr signal 301815) DMT
6.22 - (intgr 5311Cool 2MTHBC

Other peaks follow similar pattern as AQ1, fatty acids, carboxylic acids, plant sterols. Except one mistery substance at 5.79.

Please double check my work. BTW benz, screenshots might not be good enough view of the spectra? If you want me to close up on some part of some peak, let me know.
 
endlessness
#6 Posted : 12/4/2011 4:22:40 PM

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Oh btw vodsel, thanks for the offer! Atm its not really necessary, what I really need is library (or someone who has access to it and wants to help) of compounds such as full NIST 11 or wiley or whatever. If in the future I am looking for those references Ill be sure to contact you
 
Dozuki
#7 Posted : 12/4/2011 4:31:35 PM

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While I am probably of no help in reading the MS I am curious about the results. When these spec were obtained, what exactly were they from? Ethnolic extractions? Expressed juices?

Thanks,

-D.
 
Vodsel
#8 Posted : 12/4/2011 4:36:08 PM

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endlessness wrote:
Oh btw vodsel, thanks for the offer! Atm its not really necessary, what I really need is library (or someone who has access to it and wants to help) of compounds such as full NIST 11 or wiley or whatever. If in the future I am looking for those references Ill be sure to contact you


I realized the kind of library you were looking for in the following posts. I facepalmed properly. The only related links I can find in my bookmarks are this one and this other one. Unlikely to be enough. NIST libraries are not easy to hunt, but I will show up again if I stumble upon anything.
 
endlessness
#9 Posted : 12/4/2011 5:15:07 PM

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Dozuki wrote:
While I am probably of no help in reading the MS I am curious about the results. When these spec were obtained, what exactly were they from? Ethnolic extractions? Expressed juices?

Thanks,

-D.


This one was mere methanolic soaking of powdered phalaris. It's much more difficult to analyze these crude soaks because methanol dissolves 'too much', there will be loads of things from the plants that are inactive and not of interest, and that will make one take longer identifying peaks. Its much easier if one has an extract already, even if its a crude a/b extract with a non-selective solvent.

Results of this and other analysis to be done in the future will be posted in appropriate sections and reposted/summed-up here

BTW thanks Vodsel, that first link adds some good compounds to the program library! The second one i gotta explore a bit more
 
Dozuki
#10 Posted : 12/4/2011 5:33:30 PM

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endlessness wrote:
there will be loads of things from the plants that are inactive and not of interest


Thanks, that is why I was asking. It might also be helpful to know when the material was collected and the conditions that they were growing as these are definite factors in the production of alkaloids in these plants (which I'm sure you are very aware of).

This is a very intriguing project Smile

-D.
 
benzyme
#11 Posted : 12/4/2011 5:50:26 PM

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endlessness wrote:
what I really need is library (or someone who has access to it and wants to help) of compounds such as full NIST 11 or wiley or whatever.


I hear ya
unfortunately, you have to pay $$$ for annual access to databases
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endlessness
#12 Posted : 12/4/2011 6:57:06 PM

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One more very possible identification: Main peak with Yugo red @ min 7.2441 - Linolenic acid

Hey dozuki, regarding the Phalaris growth conditions (I will post all of this in the phalaris thread once we have a bit more info on the peaks and have written the relative quantity of each):

19:31:10 ‹dreamer042› the big med and aq1 I had gotten from the vendor about a month before harvest, planted in a pot and set outside in early-mid spring
19:31:30 ‹dreamer042› the yugo red I had gotten from the vendor just about a week before harvest same conditions
19:35:21 ‹dreamer042› the soil I planted it in was "happy frog organic potting soil" from fox farm, I didn't fertalize at all just watered, to dry I just left it sit out in the open air and air dry naturally
19:37:45 ‹dreamer042› I bought clones
19:37:53 ‹dreamer042› the aq1 and the big med came from c*o*m*p*a*n*i*o*n plants
19:38:15 ‹dreamer042› the yugo red came from n*o*m*a*d botanicals
 
endlessness
#13 Posted : 12/5/2011 12:06:39 PM

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The minor peak from AQ1 at 3.6149, and the major peak with yugo red at 3.5435 could be hordenine, what do you guys think?

(heres the mass spectra from nist webbook)
 
Dozuki
#14 Posted : 12/6/2011 12:06:39 AM

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In the AQ1 - 6.2071 is a pretty good match for 2MeTHBC
and AQ1 - 12.7553 has the same large peak for 5MeODMT, but the smaller peaks are cut off from the screen shot

Anderton et al lists the MS for hordenine as :

151(10), 152(6), 134(7), 121(18 ), 107(85), 77(100) = m/z(relative intensity)

From: "Assessment of Potential for Toxicity of Phalaris spp. via Alkaloid Content Determination: P. coerulescens, a Case Example": Phytochem. Anal. (1999) 10:113-118
 
endlessness
#15 Posted : 12/6/2011 1:46:07 AM

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The 12.7 is def not 5-MeO. I cant find the 2meTHBC spectra, is it in this publication you just mentioned too? I cannot get access to it...

Thanks for the help1

edit: just saw you psted in the phalaris thread
 
endlessness
#16 Posted : 12/6/2011 11:16:12 PM

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Now with full NIST version and a bit more digging around, Im learning this better. Anyways a few more identifications:

The peaks at 6.3380 Yugo red (Intgr. Signal 282044), and 6.334 (Intgr. Signal 329262) AQ1 are VERY likely n-Hexadecanoic acid (Palmitic acid), very common fatty acid. Here's the Mass Spectra vs known sample.


In yugo red, the peaks 11.9292 (Intgr signal 51866), 12.1156 (Intgr signal 25069), 12.4642 (Intgr signal 244291), and in AQ1 the peaks at 12.1106 (intgr signal 116904) 12.4669 (Intgr signal 302283) and 12.5754 (Intgr signal 13693) are all Plant sterols (example Mass spectra certain peaks vs uncertain peaks)

Another possible id: 3.5435 from Yugo red - Possibly Hordenine or another phenol-based substance (Intgr. Signal 727484) 3.614 from AQ1 - Possibly traces of Hordenine or another phenol-based substance (Intgr. Signal 21029). 1- Mass spectra of "sure peaks", 2- Mass spectra with unsure peaks + MW estimation




Peak @ 5785 in AQ1 (Intgr Signal 24802) is a mistery. The spectrum with certain peaks, vs spectrum with uncertain peaks, seems similar to caffeine, but caffeine shouldnt be there in phalaris. Caffeine has molecular weight 194, which should be the molecular ion but if you put the unsure peaks, there are some peaks of 300+m/z. And you can see the MW estimates go off if you add the uncertain peaks so I dont know what to say. Same is the case with 5781 of yugo red (Intgr Signal 72181), and the certain vs uncertain spectrum



The Intgr. Signal, if I understand correctly, is the area under the peak curve, which means the quantity of that substance. We can't make absolute quantitation unless we run some standard of known quantity to compare, but we can make relative abundance with other alkaloids in the same plant (and we can also compare both phalaris here because they were both diluted with same amounts and volumes). So from now on we should start adding the Intgr signals. to the peak information.
 
benzyme
#17 Posted : 12/7/2011 12:57:20 AM

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excellent sleuthing

the area under the curve will give you relative amounts, you may roughly determine the %age of
the compound of interest in a sample (% purity).
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endlessness
#18 Posted : 12/7/2011 1:04:30 AM

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Thanks Benz!

So if peak X has Intgr signal = 5000, and peak Y has Intgr signal = 10000, am I correct to assume that there is half the amount of substance X than substance Y ?

BTW, Ive updated my post further up with the list of already identified substances to add an image of the TIC for easier view. I will be adding mass spectra (with sure vs unsure peaks, in comparison to probable matches) and the integer signal of each peak, and in the end once we have most of this done I will edit the TIC and write down the name of substance + relative amount on top of the important peaks
 
benzyme
#19 Posted : 12/7/2011 1:19:51 AM

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yes.

and the percent purity of a peak is determined by the area under the peak divided by the sum of the areas under all peaks, X 100.
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endlessness
#20 Posted : 12/7/2011 1:08:20 PM

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Ok most substances or at least classes of substances have been identified, check my post further up. There is only one important peak at around min 5.7 in all of the 3 that seems VERY likely caffeine but I dont think caffeine is in phalaris, so Im wondering if possible contamination? Im gonna check other samples that were run the same day and see if caffeine was there in others, maybe for some weird reason we got caffeine in our samples? Any other guesses?

Here's the ratio of the significant active alkaloids (they can be compared between th different phalaris because it was same dissolution amounts):

AQ1:
DMT: HORDENINE: Possib 2MTHBC: MYSTERY CAFFEINE
14.6: 2.6: 1.1: 3.1

Big Medicine:
DMT: HORDENINE: GRAMINE: MYSTERY CAFFEINE
37.5: 13.3: 1: 44.7

Yugo red
DMT: HORDENINE: GRAMINE: MISTERY CAFFEINE
2.1: 90.3: 65.2: 9


So AQ1 has cleanest profile, but Big Medicine has most DMT.
 
 
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