Questions tagged [mass-spectrometry]
Mass spectrometry (MS) is an analytical technique which takes advantage of the mass-to-charge ratio of gas-phase ions in order to elucidate the composition of a sample.
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Are there LCMS compatible buffer systems available for the high pH range 12-14?
I want to perform chemical stability studies for different pH Values. To achieve pH Values from 1 to 6 I can prepare solutions with trifluoric acid and formic acid and ammonium formate and acetate. I ...
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How does a fragment with a m/z ratio of 94 form when benzoic acid breaks down?
Hello, I don't understand how when benzoic acid forms a fragment with a m/z ratio of 94 during breakdown. I understand it is [C6H6O]+ but how does that happen, does the ring breakdown and McLafferty ...
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Programs to view or convert unformatted Mass Spec data
I've been give mass spec data in very simple format .txt files. Each file is two columns, m/z and intensity. There is no header or anything. Are there any programs that can read this file? Or how can ...
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LC-MS/MS analysis of rosuvastatin in rat plasma two peaks
I am trying to analyse samples of Rosuvastatin in rat plasma using LC-MS/MS and ran into the problem that I get two peaks for Rosuvastatin, one after a retention time of around 7 mins and one around ...
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How to calculate carbon to phosphorus stoichiometric ratios using results from ICP-MS and CHN analyzer?
I run a few chemostats to manipulate the carbon to phosphorus ratio (C:P) of algae, which is later feed to an invertebrate. I used Inductively coupled plasma mass spectrometry (ICP-MS) and Inductively ...
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How to effectively replace DMSO with LC–MS-compatible solvent for the samples from a well plate?
I want to do LC–MS analysis of the samples from a 384-well plate where each compound (at around 1–10 μM) is dissolved in 10–15 μL of DMSO. I am worried about the DMSO dwarfing the analyte’s signal, as ...
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MS Waste Products
I'm looking for info about what happens to chemical species after undergoing MS. As I understand the process:
We have an high-energy electron beam to ionize our sample. This often leads to ...
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Total ion current normalisation of intensities derived from mass spec - does this produce compositional data?
A definition of total ion current normalisation from https://www.scirp.org/journal/paperinformation.aspx?paperid=86606, i.e. for each feature in the sample, divide its intensity value by the total for ...
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Dynamic equilibrium of Girard T-derivatized oxysterols
This is a question relating to organic chemistry, moreso than chromatography.
I am running LC-MS on various hydroxycholesterols (HC) and dihydroxycholesterols (diHC). To increase ionization efficiency ...
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in a mass spectrometer why do the ions inside the acceleration chamber not interact with each other and disturb the reading
This would be in both time of flight and deflection mass spectrometers, and this would be when you are trying to find the relative abundance of isotopes of an element.
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How can fragmentation result in a higher mass than parent ion?
I've collected MS/MS data on a (highly modified) peptide. While most of the data is fine, I've noticed that I have some daughter ions which are higher in mass than the parent ion (in this case, an ...
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Masses of atoms and molecules [duplicate]
This is my understanding so far:
Average atomic mass is the mass of an element considering isotopes and is measured in atomic mass units. However relative atomic mass is the average mass of an atom ( ...
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Resolution in mass
I'm pretty confused about mass resolution. The resolution of my instrument is 1000 and I have two masses at 85.0639 and 85.0651. So, the difference is 0.0012.
I know that (M1-M2)=M/R.
But, I'm not ...
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M- 15 Peak of 1-pentene in EI-MS [closed]
This is the spectrum of 1-pentene.
And my professor says that the peak M-15 (55) came from this process:
But how this is possible, when I tried to prove through mechanism, no one situation match ...
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Why are ions in a mass spectrometer accelerated through electric plates? [closed]
I was reading an article on the AP Chemistry course in Khan Academy about mass spectrometry, which had this:
... ions are then accelerated through electric plates and subsequently deflected by a ...
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Does the MS oxygen peak at m/z = 16 correspond to $\ce{O+}$ or $\ce{O2^{2+}}$?
In a mass spectrum, while annealing with $\ce{O2}$ of a sample in UHV, I observe peaks at $m/z = 16$ and $32 (= 16 \times 2)$. While the latter is $\ce{O2^+}$, I'm unsure what the peak at $m/z = 16$ ...
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What compounds smell like burning rubber or tar?
Background:
A couple of friends of mine live next door to each other in a 10-year old block of flats in London, UK. They say that in the early hours of the morning, a toxic smell appears in their ...
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Mass spectrum of N,N-dimethylaminoethane
I have been struggling with understanding how fragmentation works in mass spectrometry. An exercise my teacher gave me asked me to prove that a mass spectrum belongs to N,N-dimethylaminoethane, ...
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Bromine isotope peaks were observed in EI-MS, but not in ESI-MS
I have been conducting a synthesis involving 2,3,5-tribromothiophene. Because I thought that desired product doesn't have so small molecular weight, I decided to use ESI instead of EI, and so I also ...
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Why can I extract all metabolites from blood plasma with one solvent, but to extract only fatty acids I must use many solvents?
I want to do a metabolite study using GC- without derivatization and UPLC-MS (RP and NP) on samples of plasma and urine. My hypothesis is agnostic about which metabolite will correlate with the ...
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Mass spectra interpretation for monitoring Buchwald–Hartwig coupling
I am conducting a synthesis involving Buchwald-Hartwig coupling. The starting materials are 2,3,5-tribromothiophene (MW=320.83) and 1-aza-18-crown-6 (MW=263.33). I used $\ce{Pd_2(dba)_3}$ (MW=915.7) ...
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is this the reason why time of flight mass spectrometers produce a mass spectagram with mass over charge on the x axis?
Is this the reason why time of flight mass spectrometers produce a mass spectagram with mass over charge on the x axis?
I haven't used one but from what I understand, they have an electron gun and it ...
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Q-TOF vs Q-orbitrap MS data
I recently had the opportunity to analyze the same (intact protein) sample on an Agilent QTOF and a Thermo Q-Exactive, and noticed that in addition to having a moderately higher resolution the ...
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Are double spike isotopic standards suitable for quantification by isotope dilution mass spectrometry?
I would like to apply isotope dilution mass spectrometry (IDMS)* to quantify lead at trace levels. A good spike solution for the process would be the NIST SRM 991 which is an enriched material of ...
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Mass spec mass calculation difference
This is not a homework question, but for research.
I am performing mass spec on serum metabolites using Thermo Q Exactive PLUS with a HESI source which was set to a spray voltage of -2.7kV under ...
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Best method for molecular mass determination
A number of different methods may be employed for determination of molecular mass of any sample. But I want to limit our focus to the following methods,
Relative lowering of partial pressure
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calculation of relative atomic masses in the periodic system [closed]
If I now want to calculate the relative mass of c-13 based on the definition m(c-12) = 12amu, I need the q/m values of c-12 & c-13, where do I find these (I've looked everywhere on the internet)? ...
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α-cleavage of 1-pentene in EI-MS
I am studying the fragmentations in EI-MS, and this is the spectrum of 1-pentene.
The textbook says: The allyl carbocation (m/z=41) is an important fragment in the mass spectra of terminal alkenes ...
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How to find polynomial factor of relative (M+n) peak when factoring more than 2 isotopes
I'd like to ask for an extension of Nicolau Saker Neto's answer here:
What is the relative size of the (M+2) peak?
I'm trying to calculate isotopic abundances of molecules with more than 2 isotopes. I'...
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Impact of flow rate on peak areas in Mass Spectrometry
As a follow up to the discussion in comments: it's now clear that UV peaks will have larger area if flow rate is decreased, because the same portion of molecules are measured again and again.
With ...
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What is the mass of a proton?
My textbook explains that the deviation from integer atomic mass is caused by mass difference between proton and neutron, which are $1.67262·10^{-27}$ kg and $1.67493 ·10^{-27}$ kg, respectively.
If ...
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Mass spectrometer Ions with same mass/charge ratio but different charges [closed]
The mass spectrometer identifies ions based on mass/charge ratio. What happens when two ions have the same mass/charge ratio but different charges or masses?
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What is the difference of spectra of EI-MS and ESI-MS/MS?
I want to ask not difference about the principle or applicability to GC and LC, but the peak behavior of spectra. EI is hard ionization method, so there occurs many fragments, sometimes losing ...
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Why is the base peak of my MS spectra of 2,3,5-tribromothiophene at m/z=382?
I recently requested a ESI-MS analysis of 2,3,5-tribromothiophene and got this spectrum:
These are the analysis conditions:
Detector: ESI(+)
Source Tem: 150
Capillary voltage: 1.5 kV
Cone Voltage: ...
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Relative abundance of mixture in mass spectra
In MS, as far as I know, the $y$-axis, relative abundance means the number of ions detected. Then does ratio of heights of two peaks stand for molar ratio, not mass ratio
For example, given that I ...
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Does the Atomic Mass listed for each element on the periodic table reflect the relative abundances of their isotopes on Earth? Or in the Universe? [duplicate]
Somehow, I cannot find a site or book or paper explaining exactly how the average atomic masses for the elements on the periodic table are weighted....
I posted a question either here or on Physics S....
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Can ions of a pure substance be obtained in only gaseous form? [closed]
I was studying mass spectrometry where I learned that the sample is first vaporized before ionization. And ions are formed in gaseous from in an ionization chamber.
Why is there need of vapourizing ...
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Can acetone be used as a GC–MS solvent for a sample containing ammonia?
Сan acetone be used as a GC–MS solvent/diluent for a sample containing ammonia? Will there be a reaction between these two species?
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What exactly is causing analyte protonation in electrospray ionization MS?
I commonly see explanations that the presence of acid in the mobile phase is a source of protons for the analyte, and that you should be multiple pH units below the pKa of the analyte, but in practice ...
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How is electron-impact mass spectrometry data formally reported?
NMR data has the following format when reported in a paper:
How would I go about reporting my EIMS data formally? I tried looking for documents online but couldn't find anything.
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Why do I see two peaks for methyl salicylate in my GC–MS spectrum?
I ran a neat sample of methyl salicylate (CAS: 119-36-8) on the GC–MS and used $m/z~120$ as the quantifier and $m/z~92$ and $152$ as qualifiers. Below is the SIM spectrum for these ions, with two ...
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Why is atomic mass unit/unified atomic mass defined against Carbon 12?
I have searched the web all over this question and I have not really found an answer to my satisfaction. From my understanding of the topic so far, I understand that reason why concept of unified ...
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What are quantifier and qualifier ions in mass spectrometry data for GC-MS or LC-MS?
I've read that one should pick an ion peak that is unique to an analyte for quantification purposes and then pick at least 2 qualifier peaks and use their ratios to identify the analyte (or avoid ...
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Prediction/computation of mass spectral ionisation intensity
There are quite a few approaches (ranging from empirical additive rules based on presence of functional groups to full blown in silico QM calculations) to predicting molecular properties such as UVmax ...
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Why do dihaloalkanes lose both halogen atoms during mass spectrometry?
I was looking through mass spectrums of haloalkanes and found the one for 1,2-dibromobutane confusing:
The base peak is at 55 m/z, and the only fragment I can think of with that ration will be $\ce{...
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What are the benefits of using zero capillary voltage for discarding fractions in LC–ESI–MS/MS?
In the second episode of The Association for
Mass Spectrometry & Advances in the Clinical Lab (MSACL) podcast, namely Getting going with mass spectrometry : Josh learns chromatography (aired 2021-...
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Finding the structure based on spectra
I had to identify the structure of a drug based off the spectra I had. I suck at this. I gave it my best go and got some ugly structure, only to check it using a database and find out I was wrong. I ...
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Does using same calibration curve for chemical analysis introduce correlation in sample error/uncertainty values?
I am using a hypothetical case to explain my question
Let us consider a chemical analysis method A (using a certain instrument), which is used to quantify the value of a particular species b. ...
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1,5-Pentanediol MS
I'm having troubles assigning the signals m/z = 41 and 56 of the compound 1,5 pentanediol. I tried the basic fragmentations (McLafferty, loss of OH radical, etc.) but I can't figure the structure of ...
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Detecting impurities in polyethylene glycol 3350
I would like to test samples of polyethylene glycol 3350 ($\ce{H−(O−CH2−CH2)_n−OH}$ with an average molecular weight of 3350, so n is around 75) to determine if there are any impurities and if so the ...
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