Mass (mass spectrometry) Puns

I am new in mass spectrometry. I just want to ask if it still worth it to invest in specializing in mass spect in this age, and as a fresh B.S. graduate.

1. Are there any new technology being developed that is projected to replace mass spectrometry?
2. Are there other technology being developed currently that can be used in tandem with mass spectrometry (aside ofc from the usual partners of massspect like LC, IR, etc)

Hello all,

Mass Spectrometry is not my field at all so apologies if this is a terribly idiotic question but..

If I have a solution composed of 5-6 different compounds dissolved in water, where I have been given claims as to what these are and at what concentrations/ratios they are at. Can analysing a sample using mass spectrometry tell me at exactly what concentrations the 5-6 compounds are? Or does mass spectrometry only identify the compounds, but not information to determine what concentrations at say mg/ml they are?

Thanks for any clarification.

Hi Everyone;

I try to learn about mass spectrometry and I have few question about Agilent mass spectrometry try to find answers.

1- We are using (ESI) electronic spray ionasation , and acetonitril, methanol and water as a solvent,and we get chromatogram results format in sample mass minus and plus H (M+H or M-H). We don't add any acid as hidrogen donor. Where all hidrogen come from on chromatogram results?

2-ESI already ionise the sample ,so why we are looking plus or minus hidrogen on chromatogram? What is the function of hidrogen ? I know some some instrument with electron ionisation mode doesn't require any hidrogen so what's the difference with ESI and EI?

3- There are positive and negative instrument mode . If we add hidrogen to ionise for positive mode (I assume already hidrogen is existed in test environment which coming from solvent or any other sources.. my first question ) where hidrogen taken from during the negative mode analysis. If taken from my sample , can I say this " sample without hidrogen atom can't be analyzed " ?

4- There is a collision chamber which function collides the sample with nitrogen gas to fragment the sample . But with my experiments beside fragmentation I always get result exactly same mass of my sample of interest. Can I say, all may sample doesn't break down during the collision process ?

5- when I switch instrument mode between positive and negative mode which instrument part is affected. Do quadrapoll have function in this positive or negative separation process?

Many Thanks

Disclaimer: This post is a bit related to my other post regarding proteomics too.

The lab I will be joining for my Master's did a computational proteomics approached last year where the PhD student developed a software tool for "peak identification and quantification of mass spectrometry data using non-negative factorization (NMF)". I think NMF is a matrix/some kind of machine learning algorithm.

My undergrad was Biology with a specialization in Bioinformatics. Frankly, I have never heard this NMF concept nor have I developed a matrix-based machine learning algorithm before (I also have no experience working with machine learning yet, I am very excited to try)... The closest I have to working with matrixes are the abundance matrixes generated by RSEM, so I am a bit daunted. I haven't spoken to my adviser yet (my adviser is still working on this sem's finals, he's still busy), but, for all it's worth, what should I expect about this non-negative factorization, especially in relation to proteomics/mass spect?

I am guessing I will be doing a similar approach or some kind of optimization to the dissertation of the previous PhD student who graduated last year.

Additionally, what do you guys think about non-negative factorization in general for quantification and identification of peaks? Is this advisable? Is this an angle that has a lot of prospects (I am a Master's student so, if any, I wanna specialize in an idea that has a lot of prospects)? Or is this a bit outdated?

Lastly, and this is just me trying to realistically estimate whether I'd have ample of time, I only have about 3 years to complete my Master's. Considering I have no background in machine learning and only know basic python + perl programming, do you think 3 years is enough time for me to develop a software tool similar to what the PhD student did?

Can someone please help me find:

Characterisation of Commercial Vodkas by Solid-Phase Microextraction and Gas Chromatography/Mass Spectrometry Analysis

Lay-Keow Ng, Michel Hupé, Jean Harnois, Dennis MocciaJournal of the Science of Food and AgricultureVolume 70, Issue 3

First published: 01 March 1996

https://doi.org/10.1002/(SICI)1097-0010(199603)70:3<380::AID-JSFA517>3.0.CO;2-M

Thank You!

Ex: ethyl fragment weight, other misc chunks of alkyls and their structure and weights

https://users.wfu.edu/~kingag/223L/procedures-handouts/common%20MS%20fragment%20ions.pdf

basically this except with the structures drawn out

I'm currently drawing them myself but am not sure what some structures are and seem to be getting alot wrong

Understanding protein-ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)-based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct-MS method for rapid analysis of proteins directly from crude samples. Here, direct-MS enables label-free studies of protein-drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein-protein interactions, drug uptake and binding, and characterization of therapeutic proteins.

https://ift.tt/3x5fUNu

A novel mass spectrometric method for probing the flash chemistry of electrogenerated reactive intermediates was developed based on rapid collision mixing of electrosprayed microdroplets by using a theta-glass capillary. The two individual microchannels of the theta-glass capillary are asymmetrically or symmetrically fabricated with a carbon bipolar electrode to produce intermediates in situ . Microdroplets containing the newly formed intermediates collide with those of the invoked reactants at sub-10 microsecond level, making it a powerful tool for exploring their ultrafast initial transformations. As a proof-of-concept, we present the identification of the key radical cation intermediate in the oxidative dimerization of 8-methyl-1,2,3,4-tetrahydroquinoline and also the first revealment of previously hidden nitrenium ion involved reaction pathway in the C–H/N–H cross-coupling between N,N’-dimethylaniline and phenothiazine.

https://ift.tt/35EPrLf

hi labrats,

I need urgent help, this is my first time getting data for mass spec, I got a file from the facility which I find hard to decipher. If I need to calculate score of proteins expressed in comparison to control, what is the way to do it? I got LFQ intensities and some other shit in excel format. I will be grateful, if anyone can help me decipher it.

We present an ion-mobility mass spectrometry (IM-MS) study on the encapsulation characteristics of a shape-adaptable organometallic metallocage, and demonstrate that IM-MS in combination with DFT calculations constitutes a reliable approach to quantify distortions experienced by the host upon guest encapsulation.

Abstract

The encapsulation of the tetracationic palladium metallosquare with four pyrene-bis-imidazolylidene ligands [1]4+ with a series of organic molecules was studied by Electrospray ionization Travelling Wave Ion-Mobility Mass Spectrometry (ESI TWIM-MS). The method allowed to determine the Collision Cross Sections (CCSs), which were used to assess the size changes experienced by the host upon encapsulation of the guest molecules. When fullerenes were used as guests, the host is expanded ΔCCS 13 Å2 and 23 Å2, for C60 or C70, respectively. The metallorectangle [1]4+ was also used for the encapsulation of a series of polycyclic aromatic hydrocarbons (PAHs) and naphthalenetetracarboxylic diimide (NTCDI), to form complexes of formula [(NTCDI)2(PAH)@1]4+. For these host:guest adducts, the ESI IM-MS studies revealed that [1]4+ is expanded by 47–49 Å2.. The energy-minimized structures of [1]4+, [C60@1]4+, [C70@1]4+, [(NTCDI)2(corannulene)@1]4+ in the gas phase were obtained by DFT calculations.Introduction

https://ift.tt/31xdA4h

Journal of the American Chemical SocietyDOI: 10.1021/jacs.1c03321

Edwin E. Escobar, Mukesh Kumar Venkat Ramani, Yan Zhang, and Jennifer S. Brodbelt

https://ift.tt/3fU6EVG

Modafinil, a widely used psychoactive drug, has been shown to exert a positive impact on cognition and is used to treat sleep disorders and hyperactivity. Using time-of-flight secondary ion mass spectrometric imaging, we studied the changes of brain lipids of Drosophila melanogaster induced by modafinil to gain insight into the functional mechanism of modafinil in the brain. We found that upon modafinil treatment, the abundance of phosphatidylcholine and sphingomyelin species in the central brain of Drosophila is significantly decreased, whereas the levels of phosphatidylethanolamine and phosphatidylinositol in the brains show significant enhancement compared to the control flies. The alteration of brain lipids caused by modafinil is consistent with previous studies about cognition-related drugs and offers a plausible mechanism regarding the action of modafinil in the brain as well as a potential target for the treatment of certain disorders.

https://ift.tt/34nJSzW

Hybrid duplex–quadruplex oligonucleotides comprised of multiple domains have not been yet properly investigated because of their structural complexity. A new method based on native mass spectrometry (MS) coupled with a custom-built temperature-controlled nanoelectrospray ionization (TCnESI) source is introduced to investigate effects between multiple proximal DNA domains.

Abstract

Quadruplexes are non-canonical nucleic acid structures essential for many cellular processes. Hybrid quadruplex–duplex oligonucleotide assemblies comprised of multiple domains are challenging to study with conventional biophysical methods due to their structural complexity. Here, we introduce a novel method based on native mass spectrometry (MS) coupled with a custom-built temperature-controlled nanoelectrospray ionization (TCnESI) source designed to investigate interactions between proximal DNA domains. Thermal denaturation experiments were aimed to study unfolding of multi-stranded oligonucleotide constructs derived from biologically relevant structures and to identify unfolding intermediates. Using the TCnESI MS, we observed changes in Tm and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.

https://ift.tt/31Slaq4

Single-cell mass spectrometry was advanced to enable dual characterization of proteins and metabolites in identified cells in Xenopus laevis embryos. The analyzed embryos developed to normally behaving tadpoles with anatomy and visual function indistinguishable from that of their control siblings in a background color preference assay. In vivo single-cell mass spectrometry expands the analytical toolbox of molecular systems, cell, and developmental biology.

Abstract

We report the development of in vivo subcellular high-resolution mass spectrometry (HRMS) for proteo-metabolomic molecular systems biology in complex tissues. With light microscopy, we identified the left-dorsal and left-ventral animal cells in cleavage-stage non-sentient Xenopus laevis embryos. Using precision-translated fabricated microcapillaries, the subcellular content of each cell was double-probed, each time swiftly (

https://ift.tt/2QaPHNc

Hi Everyone;

I try to learn about mass spectrometry and I have few question about Agilent mass spectrometry try to find answers.

1- We are using (ESI) electronic spray ionasation , and acetonitril, methanol and water as a solvent,and we get chromatogram results format in sample mass minus and plus H (M+H or M-H). We don't add any acid as hidrogen donor. Where all hidrogen come from on chromatogram results?

2-ESI already ionise the sample ,so why we are looking plus or minus hidrogen on chromatogram? What is the function of hidrogen ? I know some some instrument with electron ionisation mode doesn't require any hidrogen so what's the difference with ESI and EI?

3- There are positive and negative instrument mode . If we add hidrogen to ionise for positive mode (I assume already hidrogen is existed in test environment which coming from solvent or any other sources.. my first question ) where hidrogen taken from during the negative mode analysis. If taken from my sample , can I say this " sample without hidrogen atom can't be analyzed " ?

4- There is a collision chamber which function collides the sample with nitrogen gas to fragment the sample . But with my experiments beside fragmentation I always get result exactly same mass of my sample of interest. Can I say, all may sample doesn't break down during the collision process ?

5- when I switch instrument mode between positive and negative mode which instrument part is affected. Do quadrapoll have function in this positive or negative separation process?

Many Thanks

Hi Everyone;

I try to learn about mass spectrometry and I have few question about Agilent mass spectrometry try to find answers.

1- We are using (ESI) electronic spray ionasation , and acetonitril, methanol and water as a solvent,and we get chromatogram results format in sample mass minus and plus H (M+H or M-H). We don't add any acid as hidrogen donor. Where all hidrogen come from on chromatogram results?

2-ESI already ionise the sample ,so why we are looking plus or minus hidrogen on chromatogram? What is the function of hidrogen ? I know some some instrument with electron ionisation mode doesn't require any hidrogen so what's the difference with ESI and EI?

3- There are positive and negative instrument mode . If we add hidrogen to ionise for positive mode (I assume already hidrogen is existed in test environment which coming from solvent or any other sources.. my first question ) where hidrogen taken from during the negative mode analysis. If taken from my sample , can I say this " sample without hidrogen atom can't be analyzed " ?

4- There is a collision chamber which function collides the sample with nitrogen gas to fragment the sample . But with my experiments beside fragmentation I always get result exactly same mass of my sample of interest. Can I say, all may sample doesn't break down during the collision process ?

5- when I switch instrument mode between positive and negative mode which instrument part is affected. Do quadrapoll have function in this positive or negative separation process?

Many Thanks

Ex: ethyl fragment weight, other misc chunks of alkyls and their structure and weights

https://users.wfu.edu/~kingag/223L/procedures-handouts/common%20MS%20fragment%20ions.pdf

basically this except with the structures drawn out

I'm currently drawing them myself but am not sure what some structures are and seem to be getting alot wrong