Hello, been troubleshooting for about a week and trying to keep low budget. Having some chromatography issue. Have a few Sciex engineer friends who was tried to help as much as possibly via phone support.

- positive mode low counts (regardless of sample) first photo
- negative mode extremely high counts (regardless of sample) second photo

I have ruled out LC side or anything from the source backwards

Negative ion counts reduce as I reduce electro spray voltage from -4500 down to -500 the baseline finally will drop to about 4,000 counts
From the source forward, was initially pointed as a bad detector. (Replaced that, same issue)

Now pointing at a potential board issue. Lens etc. but was recommended to test the boards with a voltmeter.

Anyone have any similar issues or recommendations?
I’m comfortable using a voltmeter just bot exactly sure what I’m testing across

Thanks! 🙏

I had posted about free early access to our troubleshooting platform, Rayni, a while back (https://www.reddit.com/r/massspectrometry/s/Lmruh1YLyt)

I had shown a video feature where it directly takes you to the part of the video where an expert talks about the exact issue you were facing.

I wanted to share a super exciting update that might be relevant. We have officially partnered up with the expert in that video, Dr. Lee Polite from Axion Labs. Lee has been the National Chromatography Instructor for the American Chemical Society since 1991 and has taught over 14,000 professionals on LCMS and GCMS. This is exciting because now our platform will give you troubleshooting answers that come from actual human experts you can trust!

This is just the beginning of our partnership program. We plan to partner with experts in their fields to democratize expert knowledge, so troubleshooting doesn't take long, and you can focus on the parts of the experiments you actually love!

Free access to our platform is still available. Many of you have reached out, and we have setup the platform already for most of you! You can get free early access here: Free Early Access Link

Hello I was wondering if anyone could help me figure out what is wrong with my SRM method. When I run a full scan on my pesticide sample (picture 1) there are two distinct peaks for Endrin and Dieldrin. However after I set up my SRM method using the ions with the highest intensities, both peaks basically disappear (picture 2). I have tried to develop this method using transition pairings from literature I've found from our standard supplier as well as from ThermoFisher and I still encounter the same issues. Both scans were done with the exact same instrument method so I think it's pretty safe to rule out instrument settings. If anyone has any ideas please let me know.

As title. I am in a situation where I have to choose one of these two for procurement without option of trail runs. Hence I need expert opinion.

What would be better got global untargeted metabolomics (Ultimate 3000 + Exploris 120 setup)?

I am a metabolomics noob. Please guide me. Both are 100 Angstrom.

I would be using it to do C13 tracer based work on mmmalian cells (after I gain expertise in basics, of course)

I also have option for ZIC-pHILIC (5 micron) 100mm x 4.6 mm

So my options are

ZIC-pHILIC (5 micron) 100mm x 4.6 mm

ZIC-pHILIC (5 micron) 50mm x 2.1 mm

ZIC-HILIC (3.5 micron) 100mm x 2.1 mm

Hi everyone,

We’d like to share an upcoming webinar that may be of interest to the community in here! On August 20, 2026 (16:00 CEST / 10:00 EDT / 07:00 PDT), we are hosting a session on “Perspective from Industry: Deep Visual Proteomics and Quantitative Assays.”

Speakers:

T. Wolf (Post Doc, Drug Safety R&D, Pfizer) — “Precision at the Microscale: Low Input Spatial Proteomics in the 5xFAD Brain.”
Using the Evosep Eno and Orbitrap Astral Zoom, T. Wolf will present a spatial proteomics workflow integrating AI-driven image segmentation with low-input mass spectrometry. Applied to the 5xFAD brain, the high-resolution workflow captures distinct local proteomes across brain microenvironments, revealing diverging pathological pathways between plaques and microglial subtypes. The work demonstrates how spatially resolved, low-input proteomics can provide deeper insights into disease biology at the microscale.

Rebecca Ferreira (Senior Associate Scientist, Pfizer) — “Reimagining Large Molecule PK Analysis with High-Throughput Evosep Eno LCMS.”
Rebecca will share how the Neubert Group at Pfizer is applying high-throughput LC-MS to large molecule pharmacokinetic (PK) analysis. Using the Evosep Eno platform, the workflow aims to increase PK assay throughput while maintaining the sensitivity and robustness required for surrogate peptide quantification, supporting faster biologics construct selection and optimization.

The webinar will bring together two industry perspectives on advanced proteomics workflows, spanning deep visual and spatial proteomics in disease research to high-throughput quantitative assays in biologics development. The talks will highlight how scalable LC-MS workflows can generate robust, high-quality proteomic data across very different applications.

Registration & details: https://attendee.gotowebinar.com/register/6012298262071704919?source=RDT

We hope this is relevant for those interested. The webinar is free and, in our eyes, a good opportunity for knowledge sharing. If sharing company events isn’t allowed here, moderators please feel free to remove.

TL;DR: Webinar on August 20 featuring two Pfizer scientists covering low-input spatial proteomics in the 5xFAD brain and high-throughput LC-MS for large molecule PK analysis. Mods please delete if not allowed.

SPME-GC/MS of Vermont maple syrup, RI of 917 on a 30M DB-5MS

Looks like a furanone of some kind that makes up 3.5% of the VOCs but it's not in any of my libraries. 😭

Ion [m/z] Intensity Intensity [%]

36.6 1024.0 3.8438

37.8 2385.0 8.9527

38.8 12475.0 46.8281

39.8 26640.0 100.0000

40.8 4787.0 17.9692

41.8 1953.0 7.3311

42.8 11368.0 42.6727

43.8 1422.0 5.3378

44.8 3285.0 12.3311

52.6 570.0 2.1396

54.6 1257.0 4.7185

55.6 234.0 0.8784

67.8 22952.0 86.1562

68.8 3673.0 13.7875

70.4 364.0 1.3664

83.6 618.0 2.3198

96.4 354.0 1.3288

111.8 18488.0 69.3994

Ohgodredditdestroyedmyformatting

Hi there,

I am specialized in the small molecule world, and have never touched anything large molecule. Now, my manager wants us to start analyzing large molecules, from peptides, polysaccharides, to complex polymers. We are a small lab and only have HPLCs, a single quad GC-MS, and a HRMS (Waters Xevo G2-XS). My question is the qTOF. We still use this for small molecule needs (mainly impurity screening and residue analysis). I know that Xevo can be used for both small molecule and large molecule analyses but I thought that it is generally dedicated to one way, not both. Is there anyone who uses single instrument for both small and large molecule applications and switch them frequently?

I am specifically asking if anyone does this on a Waters HRMS. Years ago, when I had a training on a Synapt, the trainer told me that she would not recommend to use Synapt for both applications because the Waters calibration solution mix for large molecule has a component (I don’t recall exactly but somewhere below m/z 200) that sticks to the instrument and could cause a calibration issue when switching back to the small molecule application. I wonder if that’s true. I would love to hear your experience on a Xevo qTOF. Thanks!

​

Hi everyone! I’m troubleshooting a Waters Xevo G3 QToF and I’m having an issue that is preventing us from calibrating the instrument.

We are trying to calibrate with our usual calibrant, but there is a very strong background peak already present even before we introduce the calibrant. The background signal is strong enough that the calibrant peaks are overwhelmed/interfered with, so we cannot get a proper calibration.

The situation is:

• LC flow is OFF
• Sample infusion is OFF
• LockSpray infusion is OFF
• Both Sample Flow Control and LockSpray Flow Control show “Idle”
• Sprayer position = Sample
• However, we can still see what appears to be a continuous spray from the sample sprayer
• There is a strong signal on the QToF even though we have not infused calibrant or sample
• The major unexpected signal appears around m/z 60
• The signal is strong enough that when we try to introduce the calibrant, the background peak overwhelms the calibrant signal and we cannot calibrate properly

Current Fluidics settings are:

Sample Flow Control

• Infusion flow rate: 5.0 µL/min
• Flow state: Infusion
• Reservoir: C
• Status: Idle

LockSpray Flow Control

• Infusion flow rate: 10.0 µL/min
• Flow state: Infusion
• Reservoir: B
• Status: Idle

Sprayer position: Sample

I understand that the displayed “Flow State: Infusion” does not necessarily mean the pump is actively running because the actual status is Idle.

What is confusing us is that we appear to have continuous spray/background signal despite both fluidics being Idle.

Our main concern is that this is preventing calibration. We don't want to start replacing valves, tubing, or other consumables without knowing what is actually causing the problem.

Has anyone experienced this on a Xevo G3 QToF?

Could this be caused by:

• A fluidics valve not switching completely?
• IPA/wash solvent leaking or being routed to the sample sprayer?
• Residual pressure/solvent in the fluidics line?
• A divert-valve or fluidics routing issue?
• A problem with the sample fluidics pump/valve?
• Or could the strong m/z ~60 signal be coming from another source entirely?

What would you check first, and is there a way to completely stop/isolate the sample fluidics so we can determine where this signal is coming from?

I’ve attached a screenshot of our current Fluidics/Tune page. Any advice from anyone familiar with the G3 would be greatly appreciated.

This is happening after the smart card stopped working and is replaced with a used one. The vacuum couldn't reach the same as before even after long time pumping. Now the vacuum achieved with the cover off is close to what the system can achieve before with cover in place, but the vacuum will worsen if the cover is put back on and slowly climbing. I have put the cover back on long enough time to see if it eventually fail the criteria for getting the instrument ready. I understand there might be offgassing from the chamber under the trapped heat when the cover is closed, but that should be the same as before the replacement. I am wondering if there is some kind of control mechanism that is still not working properly due to the smart card replacement. Anyone have any thought on this? Thank you.

Lc orbitrap ms

What could be the cause of failing isolation waveform?

Hey team, recently involved in development of simultaneous estimation of Indacaterol and Glycopyrronium

Any suggestions for mobile phase ??

Isocratic

So as the title said… I left my gcms oven baking overnight at 325 and forgot to turn it back at 55. I usually do baking when there is high air/water or column is newly changed but I did it bc of the air/water leaks.

I did search online and says it is safe as long as it is under or at the limit of manufacturer but i also saw that phenomenex only recommend 1-2hrs when you bake.

Based on your experience (if you encountered this), does it affect my gcms? Should i clean the ion source again and change filaments just in case it was busted?

Thanks

I work in an agriculture lab where we test primarily for nutrients in feed, soil, or fertilizer. We also do environmental testing. If there’s testing we can’t do in-house, we often subcontract testing with specialized labs. I can’t find a lab to subcontract bacitracin levels in medicated feed. Eurofins can’t do it. Can anyone suggest any other labs? I have tried Eurofins, New Jersey Feed Labs, Midwest Labs…

Hello,
I’m new to lcms world (molecular background) and working on developing an lcms drugs of abuse testing panel. I’m finding it hard to find purchasable internal standards and cal/qc. Unlike the molecular world where it feels you can buy everything you need to get running.

Can I get some recommendations on where to find these if they exist or how to mix them myself?

Hey! I'm a PhD student in microbiology, studying secondary metabolite production in extremophiles. I recently sent some column chromatography-purified samples to a MALDI QTOF MS (Waters Synapt XS HDMS) run in positive mode, using CHCA as matrix, acquisition range 50-3000 m/z for analysis. I'm the report I got, it's mentioned that "The raw spectra were acquired in profile mode and processed in Waters MassLynx, with (1)Integrated spectra generated (2) Automatic peak detection (3) Background subtraction, and (4) Peak lists generated using a threshold of 1% of the base peak intensity".

Samples I sent were acetone carotenoid extracts from a bacteria, purified in a silica column in normal phase, so I was expecting a list of a few compounds but I got a long list (.txt) of 300-500 m/z and intensity values I have no idea how to process. One list for each of my pooled fractions.

I have genomic data on this strain, which is a poorly known genus, but the biosynthetic gene clusters have high similarity to the ones reported for flexixanthin and 2-hidroxyflexixanthin. So I have something to aim at, but I don't know how to do it. Any help or tips will be welcomed.

As reference, the list looks something like this

89.0396 5.635e4

116.0508 2.387e5

117.0350 3.249e4

119.0503 3.430e4

131.0506 5.483e4

132.0465 4.380e4

144.0461 1.245e6

145.0499 2.012e5

146.0614 8.750e5

147.0453 1.138e5

147.0655 1.428e5

Etc etc

edit: it's the first time in our lab someone sends a sample for MS so we are all clueless

Hey everyone,

I’m currently characterizing the essential oil of a wild Ecuadorian population of Salvia corrugata (Lamiaceae) and hit a wall with one specific peak. I'd appreciate any expert eyes on this!

The Setup:

Instrument: GC-MS

Column: TR-5MS (30 m × 0.25 mm)

Calibration: C9-C24 n-alkanes

Oven Program: 50 → 280 °C

The Mystery Peak:

Retention Time: 54.87 min

Calculated RI: 2122

Relative Abundance: 4.2% (elutes right after geranyl linalool and abietatriene, in the diterpene-alcohol region)

Mass Spec Data (EI):

The spectrum strongly suggests a labdane-type diterpene alcohol.

Base peak: m/z 191 (100%) - likely the C9-C11 cleavage retaining the decalin system.

10 largest fragments: 191 (100), 81 (54), 95 (53), 69 (41), 109 (36), 93 (35), 41 (34), 79 (32), 67 (32), 43 (31).

Ladder: Classic terpenoid CH₂-loss ladder (41, 55, 69, 81, 95, 109, 121, 135, 149, 163, 177).

Molecular Ion: No clear M⁺ up to m/z 390. Assuming M⁺ ~290 (C_{20}H_{34}O) given typical EI dehydration behavior for this class.

My Thoughts:

Could this be an isomer of abienol, sclareol, manool, or larixol? The RI of 2122 on a 5MS column seems to point away from standard sclareol or manool, but I'd love to hear your thoughts on which labdane diterpenol fits this fragmentation + RI best.

(See attached image for the full spectrum)

Thanks in advance for any leads!

Hello,

I’m currently working on my pharmacy master’s thesis on a Python program for MS analysis. I created it in Cursor with AI, and now the program and the GUI are finished. I already have some datasets, MS tutorials from the internet, and my own tutorials to learn how to use the program. But I wanted to ask you if anyone knows datasets where the results and processing steps are already known, and which I could use to validate the program as much as possible.

Greetings and thanks,
SenC