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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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Removing glass fiber from samples before mass spect run?

I would like some unbiased opinions and knowledge from you all if you have time. I am measuring Phosphorus content of snail and embryo samples. I am only interested in Phosphorous content. I ...
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Examples of compounds that are hard to ionise or which decompose easily upon ionisation in mass-spectrometer

From Chemistry LibreTexts — 4.11: Mass Spectrometry: Limitations of MS generally stem from compounds that are not easily ionizable, or which decompose upon ionization. Geometric isomers can generally ...
Percival the caterpillar's user avatar
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What could lead to exaggerated positive LC-MS/MS test for tetrahydrocannabinol?

I was driving with the car and was involved in a minor traffic violation and I was submitted to a drug saliva test. The sample was analysed in the laboratory using liquid chromatography with tandem ...
centrino's user avatar
5 votes
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Mass Spectrometry Resolving Power Normalization to Average Mass

The resolving power in MS is often defined as $m / \Delta m$, or the reciprocal of the smallest discernible mass difference $\Delta m$ normalized to average mass $m$. I wonder why the normalization to ...
Selenimoon's user avatar
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I analyzed samples for arsenic with ICP-MS, my calibration standards are off. Any suggestions?

I used a multi-element calibration standard (10 ppm, with As,Fe,Mg etc.) from a vendor. I then diluted this down to get calibration standards of 0, 1, 2, 5, 10, 20, and 100 ppb. I analyzed these ...
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I can't understand a fragment in the Mass-Spectrum of Benzophenone

Summary: Took multiple Mass spectra of Benzophenone; There always is a peak at $\pu{152.2}$ that I don't understand. I made some Measurements of Benzophenone with a GC-MS. Always using EI (electron ...
Franz Emanuel Rüger's user avatar
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How does X! Tandem calculate mass from an MS2 spectrum?

I am very new to proteomics, and am using the X! Tandem tool to match MS2 spectra to a list of protein sequences. I understand that X! Tandem (and other similar tools) works by narrowing down the list ...
Philippa Richter's user avatar
3 votes
1 answer
141 views

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 ...
raptorlane's user avatar
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1 answer
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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 ...
ianis kapetanidis's user avatar
1 vote
1 answer
172 views

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 ...
Ratpricker's user avatar
3 votes
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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 ...
bribina's user avatar
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328 views

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 ...
pemb_bex6789's user avatar
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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 ...
Quantonium's user avatar
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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.
kayden's user avatar
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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 ...
mohger's user avatar
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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 ( ...
Quin Gardiner Bax's user avatar
4 votes
1 answer
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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 ...
Everson Gomes's user avatar
2 votes
1 answer
203 views

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 ...
archthegreat's user avatar
6 votes
2 answers
367 views

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 $m/z = 16$ ...
P M's user avatar
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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 ...
Rocketmagnet's user avatar
3 votes
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148 views

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, ...
warren's user avatar
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2 votes
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168 views

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 ...
Krang Lee's user avatar
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3 votes
1 answer
123 views

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 ...
Mikkel Rev's user avatar
1 vote
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77 views

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) ...
Krang Lee's user avatar
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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 ...
barlop's user avatar
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8 votes
1 answer
2k views

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 ...
oryza's user avatar
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8 votes
1 answer
69 views

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 ...
Cris's user avatar
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0 answers
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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 ...
William Wong's user avatar
0 votes
1 answer
291 views

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 ...
Qui Gonn Jinn's user avatar
-2 votes
1 answer
263 views

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)? ...
iwab's user avatar
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3 votes
2 answers
906 views

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 ...
Krang Lee's user avatar
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6 votes
1 answer
97 views

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'...
Estif's user avatar
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2 votes
1 answer
479 views

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 ...
Stanislav Bashkyrtsev's user avatar
1 vote
1 answer
429 views

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 ...
AA-lurveleven's user avatar
0 votes
1 answer
275 views

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?
Andromeda's user avatar
3 votes
2 answers
3k views

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 ...
Krang Lee's user avatar
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6 votes
0 answers
268 views

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: ...
Krang Lee's user avatar
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5 votes
1 answer
615 views

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 ...
Krang Lee's user avatar
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1 vote
0 answers
48 views

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....
Kurt Hikes's user avatar
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-1 votes
1 answer
68 views

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 ...
Pakeeza Iram's user avatar
2 votes
0 answers
119 views

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?
Rex's user avatar
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1 vote
1 answer
197 views

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 ...
oryza's user avatar
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1 vote
1 answer
516 views

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.
Thor Correia's user avatar
3 votes
3 answers
593 views

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 ...
user108649's user avatar
0 votes
0 answers
149 views

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 ...
TLo's user avatar
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2 votes
1 answer
4k views

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 ...
John Travetti's user avatar

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