r/massspectrometry

Hey everyone! I'm currently a undergrad student working with an LC-MS/MS system for an internship, and one of my tasks is to develop a method to quantify two regioisomers.

Let's call them 1PAC & 2PAC.

Separating them via LC is going to be very tricky, will require expensive columns our lab currently doesn't have.

However, one promising approach is using the different ratios of their respective major fragmenting ions. 1PAC has a major fragmenting ion - let's call it FA^(1) , and similarly FA^(2) for 2PAC's major fragment ion.

However, the catch is that 2PAC also fragments into FA^(1) but in lesser quantities (ratio is known or can be found) and vice versa, 1PAC also fragments into FA^(2) ions but also a smaller ratio.

In theory, once we know the ratios of each with the 2 ions, we could back trace the initial concentrations of a mixture of 1PAC & 2PAC using a simple system of equations (linear equations using 2 variables).

Here is a simplified version of the math:

FA^(1) = P [1PAC] + Q [2PAC]
FA^(2) = R [1PAC] + S [2PAC]

Now, PQRS can all be calculated by running known concentrations of 1PAC & 2PAC separately, and then comparing the FA^(1) & FA^(2) areas with the known concentrations.

Now, when I would run a mixture of the two isomers - I would know PQRS, and get FA^(1) & FA^(2) areas as my output.

This would leave the concentrations [1PAC] & [2PAC] as the only unknown variables, and they can be easily solved for.

I did try this with a few simple mixtures of 1PAC & 2PAC, and the results seem to be quite promising, my observed/calculated values are within ~5% of the expected values.

So my main question is - What would this 'method' of calculating the concentrations be called? I read terms such as spectral deconvolution, linear unmixing, chemometric resolution of overlapping analytes, but couldn't figure out the exact terms for it.

Thank you in advance!! And I'm definitely open to suggestions/advice for this approach if you have any 😊

I was accepted to an analytical chemistry PhD. I did a little bit of research in environmental analytical labs in undergrad, and have been working in industry these past few years. For a year I worked in an analytical environmental chemistry lab running lots of LC/GC/ a little GCMS, and the past couple years have been working as a field service engineer on dissolution and physical testing systems for big pharma. I really would like to get involved with more advanced instrumentation and become an expert at it to get to a higher role in industry, either in pharma or at an instrument manufacturer at the R&D/ project lead level, not technician level. There is a mass spec proteomics lab at the program I got accepted to that sounds extremely interesting and seems like it has a ton of application and job prospects. Any insight into the field from the experts would be greatly appreciated, thank you.

Machine: LC-msms Shimadzu 8060

Problem is we are seeing bad controls over the course of the run but not every analyte. We have done some flow through and optimization. With no big increase.

We run two different methods using two different columns.

The Second method uses APCI and one analyte on there is fine in the curve but by the end CCV it's just barely passing QC check. The Mobile phases are water and methanal.

Method 1 is ESI and there are a few on it that are not great. Mobile phases are Water and Methanal with 2mM NH4F.

The samples are acidified.

We just replaced the optic system and Q1 was cleaned. Should I clean Q3?

I have attached a tune. The one on the left is after we replaced the optic system and the one on the right was the engineer during a PM. I am just not seeing any benefit from replacing the optic system parts.

https://preview.redd.it/192ohq66362h1.png?width=1780&format=png&auto=webp&s=998bd6c6cc1dcc2357fecc200d5e188fcb695fdd

Hey guys, we are talking to Sciex about new service contracts for 7500+. How much do you guys pay in the Europe or US area and for what type of contract. You can also send me a pm.

Hi everyone,

I am doing C13 Glucose based Metabolomics in mammalian cell line samples. I am doing the extraction and all and sending samples for acquisition. I have option to outsource samples to two vendors:

Vendor A has BEH Amide column but charges twice as Vendor B who has BEH HILIC column. Rest equipment is similar.

I know BEH amide is better but is it worth spending twice for BEH amide column over BEH HILIC? How much is the quality difference?

Want to use the data for flux analysis. Untargeted data acquisition.

Hi All, No funds for travel but funds for courses being offered.

Any suggestions for metabolomics and/or lipidomics?

Hello there, we have performed a pulsed SILAC experiment to measure nascent translation. And to get a greater coverage we did extensive peptide fractionation and dia a DIA based measurement on Orbital Astral. However now we are stuck at the data analysis/ search part since DIANN is not meant for fractionated datasets.

Does anybody have similar experiences and can suggest how to move forward with searching this dataset (which was quite easy in Max quant by entering peptide fractions) . without DIA and peptide fractionation we do not get a lot of H/M precursors at early time points which is where we believe our interest lies.

Any help is highly appreciated.

Howdy yall!

Sick of spending $120-$400USD to send to Janoshik + the $115 in shipping.

Are there any reputable testing options within Canada? Ive found absolutely nothing.

Thanks!

I am having issues tuning my TSQ 8000 GCMS after PM. The system behaves as if ions are not hitting the detector at all.

Who do you trust as your (UP- hopefully) LC (or GC) counterpart?

I trust Waters for UPLC (and damn they just make the best C18 columns these days) but I am underwhelmed by Ultimate or Vanquish. My preferred MS is Orbitrap machines (Fusion, QE etc), but I feel the best would be a good marriage between the two.

GC it's Agilent all the way, but I could be convinced if someone has a good experience.

LOOKING FOR Laboratories that offers:

- Gas Chromatography (GC) for ethanol
- High Performance Liquid Chromatography (HPLC) for reducing sugar analysis

within Luzon (better if nasa manila/ bulacan/ cavite/ laguna)

May alam po ba kayong laboratories na nag seservice ng ganyan, at estimated price sa mga ganito? thank youu po!

Hello,

In my lab we have Thermo Fisher Vanquish HPLC + TSQ Altis MS. We normally run a system suitability sample (SSS) before our real sample analysis and today, the SSS gave extremely inconsistent data even though the injections were from the same vial.

Last week, we had LCMS preventative maintenance (PM) done where the field service engineer at the end did recalibrations with the CalMix and everything looked good.

Before the PM, the data from the SSS injections was very consistent, with less than 5% coefficient of variation. Today, post-PM, everything is a mess. The peaks from the injections from same vial are eluting at different retention times, inconsistent intensity, etc.

The Tune file in Chromeleon checks everything green and the temperature, pressure, vacuum etc all look stable. There were a few leaks as well from different Viper connections but those were handled.

Any leads would be appreciated!

Dear MS Community,

We recently inherited a Waters Xevo TQ-GC from a nearby company, and I just had the time to setup the instrument and put it on the bench. It's a 2021/2022 system with an Agilent 8890 and PAL RSI 85 autosampler. Unit looks brand new, and the GC counter has fewer than 100 injections total. We were told by this company they purchased the unit for an R&D project that never took off - given we're academic, we were very happy to inherit the instrument.

I'm having a hard time figuring out how to tune the instrument as the unit doesn't appear to generate any ions. I've tried to: clean the inner and outer source components (making sure everything was re-aligned properly), replaced filament 2 (it didn't ignite / produce current), played with all source settings, changed the PTBFA to a new bottle, and more. I was able to produce a few ions (69 and 219 m/z) when the source pressure was higher; however, I've been unable to replicate this after the unit has pumped down. I have helium as the carrier gas at 1.4 mL/min through a DB-5MS column and argon into the collision cell. After a lot of fuss, I was able to get the autotune at 219 m/z to work for 10-15 minutes; however, after the pressure further reduced, I cannot see the 219 ion at all, nor the 69 m/z ion. I never saw the 502 ion needed to calibrate the MS.

I have virtually no experience with the Waters GCMS nor LCMS platform, and given the instrument is like-new, I'm sure I'm missing something simple here. I'm attaching some screenshots for additional information. That blip of signal on the TIC pane on the last screen is when I leave the PTBFA reference gas off for 10-15 minutes and then turn it back on. This makes me think there's possibly a leak in the PTBFA delivery mechanism?

Any help or guidance or recommendations on who to contact would be very much appreciated.

Thank you.

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Hi everyone, I’m trying to understand real pain points in GC-MS/LC-MS data analysis workflows.

For people who regularly process GC-MS or LC-MS data:

What part of compound identification is still most manual or annoying for you?

For example:

• choosing the right peak
• background subtraction
• extracting a clean spectrum
• NIST/library matching
• checking false positives
• integrating peak area
• batch processing many samples
• making final compound tables/reports
• explaining why a compound ID is reliable

I’m especially interested in workflows where you look for specific compound groups, such as hydrocarbons, polymers/plastic markers, biomarkers, contaminants, metabolites, etc.

What software do you use, and what still feels slow, confusing, or error-prone? I'm doing a case study, so would be really grateful, if you guys reply :)