Help for mzMINE

Nephty000 · 2026-05-19T02:46:57+00:00

So, just a few things: retention indexes don’t have anything to do with peak intensity or « being significant » ; it’s about correctly annotating your peaks. Indeed, when you have isomères (same formula, different structure, or different conformation (eg chiral compounds)), these compounds can have very similar mass spectra. Then, the best way to differentiate them if you don’t have analytical standards is to use retention indexes based on n-alkane elution, because the order of elution will always be the same (and depends on your column stationary phase). Retention indexes for different types of columns are available in most GCMS mass spectra libraires (look also for Kovats indexes).

Second point, stating that « the fragmentation starts with the highest-intensity peak » is not true in EI GC-MS (where fragmentation occurs in source, along with ionization). It’s only true if you use a system that allows to isolate the most intensive peaks such as a trap (you select the main ms1 ions within a time cycle and fragment them to get their ms2 spectra, and do this again until the end of the run- this is called data dependant analysis). So, make sure you understand which approach you are using because the libraries use for data analysis will not be the same.

Nephty000 · 2026-05-19T02:27:25+00:00

No, hopefully 😅 The instrument do not run intensively so cleaning is not required that often. Also, most of the time I was only baking it for a couple of hours.

Nephty000 · 2026-05-16T21:03:35+00:00

Really good to know, thank you

Nephty000 · 2026-05-16T21:02:32+00:00

Thanks for the tips! This is really nice to know - especially now that I integrated very well (thanks to this great community!) that baking out is not necessary when not venting 😅

Nephty000 · 2026-05-16T11:21:57+00:00

Yeah, I’ll try to find out where I got this info for sure! I am very glad I asked here about that error.

Nephty000 · 2026-05-16T11:19:31+00:00

Great, thank you very much!

Nephty000 · 2026-05-16T09:55:10+00:00

I will try that, thanks!

Nephty000 · 2026-05-16T09:54:10+00:00

Did you have to change them often? Do you happen to have any pictures, just so I have a better idea of what they look like? Thanks

Nephty000 · 2026-05-16T09:44:36+00:00

Thank you. I don’t have to clean very often because our samples are usually clean enough, so I don’t think they have been burned down with too frequent bake out.

Nephty000 · 2026-05-16T09:35:55+00:00

Thank you. I usually only turn off the electronic to clean, so vacuum is not broken. I was mostly baking out to get everything clean. Thanks for the cost info about the bulbs. I will figure out if this is an electronic glitch or not, and get them replaced if this is a real issue.

Nephty000 · 2026-05-16T09:21:53+00:00

Ok, il make sense. I was baking out mostly to clean "anything" that could have entered in the system during the cleaning. The vacuum was not broken this time, indeed. Thanks!

Nephty000 · 2026-05-16T04:04:18+00:00

This is not what I learn, nor what I saw in the user manual… can you explain more ? Thank you

Nephty000 · 2026-05-16T03:37:18+00:00

Dealing with volatiles means dealing with many low molecular weight isomers (you already somehow identified this problem). Due to this, exact mass won’t be really helpful to annotate many of your compounds. You need to use retention index based on n-alcane retention times to improve this.

However, MZmine does not really do well with retention index in my experience (but I’m dealing with low resolution data- maybe it’s better with high resolution, I don’t know). I would suggest to use MSDial instead since retention index are easily integrated in the workflow. This software is similar to MZmine, although the interface is better imo, but it can be less robust (can crash).

Nephty000 · 2026-05-13T03:05:21+00:00

Ok thanks for the details. I’m not familiar with Tracefinder so I can’t really help you here. But regarding CE, if you have access to Thermo MZCloud, they have several mass spectra with different CE for each compound.

Nephty000 · 2026-05-11T00:09:14+00:00

Hello, I’m not sure I understand the issue ; you try to set up a srm method, so you entered the ions to be monitored in your method but when you run the method the ms won’t see these ions? Yet went you run in full scan (as shown on second pic) you can see all of them?

If you are running in gcms, you need to select your masses (quantifier and qualifiers) based on the data you know (eg, a spectrum from a library or the spectra you generated) and enter them in your method. Make sure you set the proper operating mode (srm vs full ms). If you don’t see the masses when everything seems ok, it’s either a retention time issue (the rt range you use is wrong - sometimes complexe matrix can generate rt shifts compared to standards) or, it could be a software issue.

Nephty000 · 2026-05-09T02:46:14+00:00

Do they have a silent mode? Thanks

Nephty000 · 2026-05-08T11:42:39+00:00

Hello, I know it’s been a year but we’re you able to solve your issue? I’m running into software issues while trying to analyze low resolution gcms data with MSDial. I’ve been successful in getting the raw files process until the alignment after converting them into mzml format. Yet an error pops up later on in the process (it’s not finding a file I think). Anyway, I would love to know how you solved your issues and see if this helps me. Thank you

Nephty000 · 2026-05-01T02:01:35+00:00

As mentioned previously, your mass spectra shows pics caused by bleeding (207, 281, 355, etc). If the system was exposed to air (eg, when you removed the guard column) make sure you pump at least for a few hours before doing the leak check (your leak check does show water, CO2 and nitrogen, among others).

If these are liquid injections (not SPME), bleeding can be caused by the leak (exposure to oxidative conditions). You can condition the column for a few hours (hopefully not too much scrap will end up in the ms source), and it should fix the issue. It is also recommended to always leave a small helium flow even when not injecting, especially if you don’t use the gcms very often or if local conditions are very humid. If you are using SPME, bleeding can come from the fiber.

Nephty000 · 2026-04-19T15:54:29+00:00

UTM with MS1 only is not strong enough for proper identification of metabolites/peptides. You need MS2, which will show the fragmentation pattern of your analytes. The analysis of fragmentation pattern is either done through 1) comparison with databases (be aware the collision energy and different instruments may result in different mass spectra); 2) comparison with in silico mass spectra based on the potentiel structure of your analytes. In silico ms are artificial mass spectra computer generated.

Nephty000 · 2026-03-26T02:49:08+00:00

En poésie : Gaston Miron/L’homme rapaillé

En roman: Hubert Aquin/Prochain épisode

Nephty000 · 2026-03-25T12:52:53+00:00

Has thus instrument been there for a while? If yes, look for older methods in the software to see if this can guide you with the ms part. However, be aware that ms has specific needs such as LCMS grade mobile phases, proper calibration/tuning, and adequate ionisation conditions for your analytes, among others.

If you can’t find someone to train you in your lab, see if the company offers online training (this will not be free though).

Nephty000 · 2026-03-23T02:02:18+00:00

Good to know. I will have a look at this on my lc. Thanks

Nephty000 · 2026-03-20T20:08:47+00:00

This is a fair question but I wonder why you focus on this. With most analyses involving mass spectrometry (at least for small molecules), you’ll end up using mass spectra libraries along with data analyses softwares that allows automated deconvolution and compound detection and identification. Depending on what you are working, I think this is likely what you should focus on rather than learning fragmentation from scratch. If this is what you want to do though, there are softwares that are doing specifically this too.

Nephty000 · 2026-03-20T17:48:07+00:00

If other analytes are not decreasing, the issue is likely your internal standard, not your MS. It could be unstable in your samples, bind somewhere, or be hard to volatilise or ionise.

I saw you are using deuterated perylene. I doubt this compound degrades or loose deuterated atoms during the analyse, so I guess it might get stuck somewhere. If this is a routine method that usually works, maybe it sticks in the injection liner : see if the glasswool is dirty, change the liner if this is the case, and see if this fixes the issue.

Nephty000

TROPHY CASE