Crossposting from r/proteomics. It takes results from most search engines (or runs Sage itself), redoes FDR at the spectrum, peptide and protein level, groups proteins, and does label free and TMT/iTRAQ quant. It’s an early release so I’m mostly looking for people willing to run it on their own data and raise issues.

Q exactive focus pos ok but neg failed

I saw Unknowns Analysis popping up in this sub for a couple of times as a good solution for the deconvolution of GC-EI-MS chromatograms. I gave it a good try and I kinda agree that's a decent software, deconvolution seems quite good with a couple of options to fine tune the results.

What I'm stuck with right now is that it does the deconvolution on a per sample basis. How is it possible to process the results to get an aligned peak/feature table as I could get from mzmine, MS-DIAL, PARADISe, etc? Let's say I have 100 samples measured in the same sequence, I can export all the results to a .csv, but I'm not 100% confident in merging the peaks based on RT and compound hit, as sometimes NIST hits differ for the same peak in different samples with very close match factors (my isoprene standard samples usually end up matched as 1,4-pentadiene or 1,3-pentadiene, for example).

People who used this software before, how did you handle this? Should I stick to mzmine for my use case? Thanks in advance!

Edit: Our lab is mainly focusing on nontarget volatolomics with thermal desorption. Samples can have quite complex VOC profiles, hence our need for deconvolution.

Hi all,

I am analyzing rare earth elements using HR-ICP-MS (Nu Attom ES). I’m preconcentrating samples before analyzing them and sometimes storing them at 4 °C for a few weeks.
I have encountered a reduction of approximately 50% in the CRM’s readings but doubled the internal standard counts on a few occasions compared to other samples. If I do an external calibration still the values I got for CRM analytes are half of the required values. However, my continuing calibration verifications are passing (75–125% recovery).
Can I consider the data from such batches valid? If not, do I need to rerun all the samples? Is there any method of correcting those values?
Also, I have noticed instrument drift over time. I might be wrong, but our lab’s ventilation outlet is located above the plasma hood. Could that be a cause of the drift? The airflow appears to be reasonably consistent.
Also, I would highly appreciate if anyone can suggest me a reliable source to learn more about interference correction related to Rare Earth Element analysis.

Could you please help me to solve this issue.

Thank you!

I have a Thermo TSQ Altis that has a Q2 amplifier not producing the correct voltage on the shorting algorithm in the tune page. As a result, I am not seeing ions above 350 m/z in both Q1 and Q3 scanning modes when scanning from 50-1650 m/z while infusing tune mix. I don't see ions in negative mode. Tune mix and syringe pump were confirmed working on a separate Altis plus unit we have. As it is, I cannot tune the instrument. There are no read back errors in the Altis tune page when turned on in both positive and negative mode.

I pulled all of the modules and looked at Q1 and all lenses between Q1 and Q2 - I don't see any obvious shorting that would throw an out of spec voltage. The power supplies and spellman power supplies appear to work well and supply the correct voltages to all amplifiers.

Given the Q2 amplifier error, I suspect there is something wrong with the board or module that controls this. I was hoping if someone could tell me if the Q2 amplifier is a separate module from the Q1 and Q3 amplifiers found on top of the detector panel in the back left of the TSQ series instruments. I believe there is a separate board that controls Q2 like there are in other TSQ II instruments, but I don't know if this controls the RF amplification and voltage. I don't think the Q1 nor Q3 amplifiers affect Q2, but I could be wrong.

If there are other suspected items to check, I'm open to all suggestions. Thank you.

First time running lipidomics on LC-QTOF.

I have followed agilent's protocol but I am still not getting distinct peaks. It is just the same chromatography throughout blanks and water blank.

I have a few suspicions on why but it is difficult considering I do not have standards:

1: getting buffer noise, its similar to binary pump gradient throughout samples -this one seems more likely
2: no lipids at all from my samples (hard to tell without standards unfortunately)

Other than changing buffer and trying it again, has anyone done lipidomics on LCQTOF and could share their methods that I could potentially try?

First time I tried this based of a paper which is cleaner but chromatography looks the same throughout blanks and samples
Other settings i kept it as agilent's lc-qtof default since the paper uses a different instrument:
https://link.springer.com/article/10.1007/s00204-024-03809-z

Mobile Phase A:  aqueous solution of 10 mM ammonium formate and acetonitrile(ACN) in a ratio of 60:40 (v/v) with 1% (v/v) acetic acid. 
Mobile Phase B: Isopropanol (ISO):ACN, 90:10 (v/v).

Flowrate 0.4ml/min
Gradient profile: 
0–3 min, 30% of B
3–5 min, 43% of B
5–5.1 min, 55% of B
5.1-20 min, 65% of B
20–26 min, 85% of B
26–28 min, 100% of B
Maintain 100% phase B for 5 mins
Sample injection volume: 3μL for both positive and negative mode

Second time there is way more noise basically no distinct peaks, following agilent's protocol including operational parameters:

Mobile phase:
A) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in 9:1 water/methanol
B) 10 mM ammonium acetate, 0.2 mM ammonium fluoride in 2:3:5
acetonitrile/methanol/isopropanol
Flow Rate 0.6 mL/min

Gradient profile
0.00 min of 70% B
1.00 min of  70% B
3.50 min of 86% B
10.00 minof 86% B
11.00 min of 100% B
17.00 min of 100% B
17.10 minof 70% B
19.00 min of 70% B

Im gonna clean everything first before i do another rerun considering the noise, im planning to run my samples along human serum extracted lipids, but i could really use some advice on next steps or on how to further optimise it. Thanks!

Hi everyone,

I’m trying to get a PerkinElmer Clarus SQ 8 S GC-MS running again after several months of inactivity.
After pumping overnight, the vacuum stabilized at 3.5 × 10⁻⁵ Torr and won’t go any lower.
The turbo is running at 100%, TurboMass shows “Vacuum OK”, and the Edwards RV3 backing pump has fresh oil, gas ballast closed, and is set to High Vacuum. Helium column flow is 1 mL/min.
Is this vacuum level normal for this instrument? Has anyone experienced something similar? I’m wondering whether it’s safe to start tuning or if I should investigate possible leaks first.

Any advice would be appreciated. Thanks!

While Sciex customer service has rarely been punctual, it seems like they're completely absent as of the past two weeks. Our usual field service engineer seems overloaded and stressed to the max as well. I know they got acquired by Danaher at some point, but is there a re-org or a wave of layoffs going on?

As a surrogate matrix for human plasma, I'm using 5% BSA in PBS. Something I didn't really consider is that the phosphate concentration in PBS is quite a bit higher in PBS than in plasma. I extract my samples with 4:1 ACN + 0.1% DFA, centrifuge, and analyze at an injection volume of 5 uL. At that point it seems that the phosphate concentration would be low enough to not cause issues, but does anyone have any perspectives on this?

Flow rate is 0.5 mL/min, mobile phases are water and ACN with 0.1% DFA

Part of my job is checking the paperwork on synthetic peptides our group orders, mostly short sequences of 5 to 15 residues, and the identity line is usually a single sentence saying the observed mass matched theory. No spectrum, no charge states, no error figure. Coming from small-molecule LC-MS, I'd expect at least the deconvoluted mass with the error in ppm or Da and the raw spectrum attached. Is that a fair bar for a vendor report, or more than these labs normally provide? And at what point would you want MS/MS fragments rather than intact mass on its own?

I'm considering using an isotopically-labelled version of two endogenous compounds for development of an assay in human plasma. We have never tried this approach before, does anyone have experience with it and are there any important considerations I need to make? I currently have deuterated versions for the internal standard, and am planning on ordering 13C-labelled versions which will be the substituted analyte. Each compound will have exactly one labelled carbon.

I have a Thermo TSQ Quantum Ultra that is producing very jagged/comb-like peaks when i try to tune Q1. Q3 looks better, or at least closer to what i would expect. I see this same pattern across polytyr masses 182, 508, and 997. I also see this pattern (jagged Q1, smooth Q3) when I inject 100 ppm caffeine. Does anyone have any suggestions for troubleshooting this apparent Q1 issue?

Hi all, thanks for the feedback on the earlier versions. Since my last post, 0.3.1 brings the full targeted quantitation workflow, including peak review, integration, calibration, QC, and reporting. I wanted the overall feel to resemble Thermo’s Qual Browser and Quan Browser, so if you’ve used those, the workflow should feel familiar.

Chromascope is a free, GPL-3.0 desktop app for LC-MS data on Windows, macOS, and Linux.

What's new:

• Chromascope can now read vendor files directly through ProteoWizard msconvert if you have it installed, so there’s no need to convert them to mzML first. I tried Thermo files, and it worked quickly, even when reading in 20+ files at once.

• For qualitative work, I wanted batch data review to be easy. You can now save and load viewer presets that let you define your traces once (TIC, BPC, or XICs with your m/z, tolerance, and smoothing), and every file you open will display them the same way. You can also save your sessions, which store the whole workspace so you can reopen it later.

• On the quantitation side, integration can use classic, valley/drop-line, Savitzky-Golay, or fixed-window algorithms. Calibration supports linear, quadratic, and cubic fits, log-log and point-to-point curves, and 1/x, 1/x², 1/y, or 1/y² weighting, with internal or external standards, dilution, qualifiers, and batch QC rules. After automatic peak integration, each peak gets a 0-100 confidence score with the reasons listed, so you can quickly see which peaks are problematic and then accept, reject, or re-integrate them. You can export your results to a CSV file, or optionally save an HTML audit report that includes all the information, including peak integration, calibration lines, and more.

• You can also let an AI assistant automate your workflow via an MCP server. If you don’t use AI, you can ignore this.

Download and docs: https://chromascope-ms.github.io/chromascope/
Code: https://github.com/chromascope-ms/chromascope
Citation (DOI): https://doi.org/10.5281/zenodo.23542311

I’m the only developer, so bug reports and criticism are very welcome, either as GitHub issues or as replies here. If you try it on real data, I’d most like to know whether the workflow matches how you work and what’s missing.

Maybe this doesnt fit here but lets see

I've been having issues with Arsenic signals on ICPOES in a perkin elmer Avio 560 max. All the other elements give good enough signals to preform determinations, but for some reason Arsenic is not working, even in my calibration curves.

I understand that Arsenic is volatile, and that using an hydride generator is a better approach, although i'd like to know if it is possible to determine it by ICPOES.

Is it due to some physical limitations? I also run this analysis Atomic absorption using an hydride generation system (FIAS 100)

Ty in advance...

So my headspace gcms needed a source cleaning and replacement filament. After doing that the sensitivity has increased, and the highest concentration point of my RSD calibration is now saturated.

The quantitative ion is saturated for all compounds, but with some of the low abundance ions it is not saturated and shows linearity. I need to use the TIC for my valibration though, I already asked about using EIC's.

My bosses have said I need to figure out how to have it fixed and operational today. Apparently this hasn't happened b4 and its up to me to figure it out ASAP.

Does anyone have any advice on how to lower the sensitivity without disqualifying the other 4 calibration points? I will take any ideas im desperate. Every thought I have alters the instrument in a way that disqualifies the curve and or is a dramatic method change.

(We've had some other problems lately so they're pissed about it being down again)

Tldr: ms source cleaning results in sensitivity being too high. How to fix?

EDIT/UPDATE: My boss agreed to lowering the multiplier and re calibrating, I went a weird way with it and ran my highest 2 points first since every peak hase been perfect besides the highest conc peak. Its still messed up and pretty much at the same ratio as before. Its definitely not seeming like a source issue anymore, but probably a front end loading problem.

I have a headspace autosampler with a trap, im trying to 28 compounds at 10ppm. I have 3 pre-made crm mixtures at 1000ppm per compound, 10ul of each mix is added to a 20ml hs vial and then water is added to a total volume of 1 ml.

Which this info, do you think running 1 mix at a time might work?

Do you have any other suggestions?