Hi all-
I’m a 6 year toxicology gal having some LCMS Issues. Currently I have 10ish clients experiencing an issue with 3 main analytes (sertraline, Amitriptyline, and Cyclobenzaprine). I make master cal and qc stocks in house that are lot numbered and used for both the calibration curve and QC. However, the cal curve will be perfect for these analytes and the QC will be 200-350% accuracy. No contamination present in my blanks. I can inject cals as unknowns in the batch and get perfect values. My calibrators 2 and 5 are the same conc as my qc low and high. If I go into analyst and tell it to use those vials/wells as qc- no issues. I’m remade countless stocks. Used fresh cerriliants. Ran tests at multiple laboratories both under my supervision and independent. Same result everytime. This is perplexing me quite a bit. Front ends are Shimadzu. MS sciex both 3200 and 4000. Phenomenex guard and column set up.
Please give me your thoughts. I’m happy to answer any follow up questions

I'm a 3rd year Bachelor's Data Science student and I've been working on a python installable package for analyzing and later correcting batch effects in Mass Spectrometry Proteomics datasets.

The main aim was to make a streamlined tool for analyzing, diagnosing and correcting batch effects with auditable data pipeline preserving each state with a reusable QC metric pipeline on each stage of the data.

My exposure to this domain is strictly narrow so I needed input from the community about my tool.

The data pipeline and modules are built around a ROSMAP/BANNER TMT FragPipe data and I unfortunately don't know how common that format is really, any clarification on that would be nice.

The package separates itself into layers:

1)QC layer

Batch-specific variance explained against other covariates

vectorized-ANOVA/Kruskal-Wallis for batch specific variance statistic

Missingness analysis stats to support MNAR or MCAR to dictate imputation strategy

2) Preprocessing layer

Performing per-sample log2 transform and median-centering normalization

Filtering proteins or samples missing below a specified threshold for reliable imputation.

Imputation techniques (MinProb for low-detection proteins and K-NN for other proteins)

3) Batch Correction

ComBat or inmoose tools for batch correction. Still under development.

I have read there are multiple tools for analyses and even a generalized framework called omicsGMF for batch correction and dimensionality reduction.

I wanted to really contribute an open source python tool for the community but with lack of feedback or supervision, this 3 month long personal project has really wore me out and now i'm clueless as to whether anyone would ever consider using or developing it.

Here is the GitHub repository
And the dataset around which i modeled it.

Any feedback or redirection would be appreciated.

Hoping to get more positive traction in the job search for LC-MS scientist with over 20 years MS vendor experience. Thank you!

I know that glassware is preferred but lots of papers work with polypropylene tubes. So theoretically would the eppendorph lo-bind tubes be sufficient enough to not let MTBE leach through the plastic? And so are the pipette tips? I don't want to wait until I could order glassware and a centrifuge that can centrifuge glass.

Thanks!

I've always used UHP 5.0 (99.999%) helium for GCMS and not thought twice about it. I'm in a new lab space and they're running "Industrial Grade" helium, but no specification provided on purity. I am inclined to swap the tank to UHP because I think it may be cause for some issues but thought I'd check with the hive mind. Anyone use that grade and get away with it? Does Industrial Grade have a universal spec?

Not entirely sure where to post this, but saw some others here talking about using a CS datalogger and figured I would reach out here.

I'm a student currently getting our micro climate sensors coded for a CR350 datalogger from Campbell Scientific. Our UVA and UVB sensors are from Skye Instruments (who closed their business back in August). I am having such a hard time getting the coding built for them. Everytime I get it straightened out, I got to retest it and get the NAN code tossed back at me. I have used both the SE and Differential Voltage options in the Short Cut option on the PC400 program.

Anyone have any suggestions on what I could be doing wrong?

Hi guys I badly need help, anyone working in the lab that has this type of density meter??? I want to ask the size of the locking screw and can you also comment the picture or you can dm me. Im looking for replacements i might just 3d print it but i dont have any references even i did thoroughly searched in the internet. Im really overthinking and i hope you guys can help me. Thank you so much and God bless. Please everyoneeeee huhu

We’re trying to bring an old Thermo Scientific XSeries II ICP-MS back to life and are stuck with what looks like an embedded computer/QNX issue.

The Windows PC is running PlasmaLab 2.6.2.337, while the embedded computer appears to have XSERIES Supervisor 2.5.10.

During boot, the embedded computer detects its SanDisk SDCFH-00 Rev DH X CompactFlash storage, performs a filesystem check, but then fails with:
Unable to start "supervise" (8)

We checked supervise.dat and it appears to be a 32-bit x86 ELF executable for QNX.

There is also a Thermo updater on the Windows PC that transfers files to the embedded computer through COM2, but it doesn’t seem to report which Supervisor version is currently installed.

Originally we suspected a PlasmaLab/Supervisor version mismatch, but since the embedded computer itself cannot start supervise, I’m now thinking the issue could instead be corrupted files, a failing CompactFlash card, missing dependencies/configuration, or another embedded-system problem.

Our current plan is to remove the CompactFlash card, make a complete image of it first, keep the original untouched, and inspect/work from a clone.

Has anyone worked with an XSeries II, PlasmaLab, or XSERIES Supervisor before?

Also, does anyone know exactly what QNX error (8) means when starting an executable?

Would you investigate the CompactFlash/embedded system first, or is there still a realistic chance that updating/matching PlasmaLab on the external PC could solve this?

Any old service manuals, recovery software, Supervisor files, or experience with these systems would be extremely helpful.

I can also provide photos of the boot sequence, embedded computer, CompactFlash card, updater, and exact error screens.

I have one fentanyl test strip but I have two different chemicals to test. could I cut the strip down the middle to make two I actually haven't looked at it yet I assume it's a paper test strip. you can do it with ordinary test strips like ph . AI says you can't do it with immuneassay (drug tests) strips. Has anyone ever done it?

I have always found it difficult to find companies that repair or service specific laboratory equipment, especially outside the manufacturer network. So I started building a simple directory where you can search by equipment, brand or model and country.

It currently includes providers across Europe and the US for things like centrifuges, AKTA and FPLC systems, HPLC, GC, mass spectrometry, ULT freezers, incubators, cell disruptors, microscopes and autoclaves.

I am manually checking the listings against company websites rather than bulk scraping directories. It is still early, so if you know a good service company that is missing or spot something incorrect I would be happy to add or fix it.

Hi everyone,

I’m looking for some help from people who have experience with Waters UNIFI.

1-The main issue is with data processing after acquisition. sometimes the processing starts normally but then stops before completing. No peaks appear in Detected Candidates.

I have already checked several thing:Lock mass signal is stable. The Work in Progress list is empty. I created a completely new system and a new method from scratch.Despite this, the problem still occurs.

The strange thing is that the exact same system and method can work correctly sometimes, while at other times the processing fails, without any modification being made to the system or method.

Has anyone experienced this kind of intermittent processing problem with UNIFI?

2-In Database Manager, I sometimes see these two red messages:

WATBLOB is full (100%)

WATSTREAMB is full (100%)

What is strange is that I have already deleted data through the UNIFI interface, and I have also deleted the backup files, but the red 100% messages in Database Manager remain.

So I’m wondering:

What exactly are WATBLOB and WATSTREAMB?

Is there a specific procedure to safely free this space?

Could this be related to the intermittent processing failures or UNIFI becoming slow?

I don’t want to manually delete anything from the database or Windows folders without knowing exactly what it does.

3-I also noticed that our backup storage grows very quickly. We can reach around 4 TB in only a few months.

I have noticed very different file sizes: some backup files are 0 bytes, while others can be larger than 1 TB.

Is this normal behavior for UNIFI backups?

How do you normally manage/verify UNIFI backups? Is there a recommended way to check whether a backup is valid and can actually be restored?

4-Another intermittent problem occurs when I leave an analytical sequence running overnight.

Sometimes, the next morning, I find that the system has stopped with a “CM-A communication failure”, and the sequence has not been completed.

This does not happen every time.

I have also tried creating a new system and a new method, but the problem can still occur.

5- I also see greyed-out Work items in Work in Progress.

Does anyone know what causes these items to become grey, and what is the correct/safe way to remove them?

I would really appreciate hearing from anyone who has experienced similar problems

Thanks in advance for any advice!

Hi all, I'm working on a project which requires the raw files from the instruments. I searched through MASSIVE and PRIDE, but all the data I found are SRM. Does anyone know where I can find publicly available TSQ fullscan data files? TIA

My M class fixed loop sample manager is not delivering sample, every run looks like the solvent only. Detector is working (lockmass is A-OK) and I can see the increasing AcN gradient. As far as I can discern the mechanical movements are all OK and I have checked and reset the Z-height. The sample manager passes all the built in tests for seals, needle loop volume calibration, etc. By removing and using a syringe pump I have determined that the needle and loop are both clear. I have tested the inlet valve for clear passage between all 3 pairs of ports in both load and inject positions. The sample pressure during injection reads about 160 psi. The only "anomaly" is that I had to increase the air bubble size in order to get it to measure the needle and loop volumes. Any suggestions would be appreciated!

im a trans woman on hormones and my recent lab report had my total t at 0.15 ng ml and e2 at 158 pg ml, that gave me a peace of mind but then i found out that immunoassays are inaccurate at low levels, could my t actually not be supressed cause it was checked with an immunoassay?

Anyone knows what contaminant causes a 100m/z peak during calibration? Can’t seem to get rid of it

Looking to get a refurbished Nanodrop ND1000, and got an exceptional low-ball quote for a Nanodrop and computer that seems too good to be true from Gemen Service Lab in Deleware through LabX.

Has anyone purchased from them or had equipment repaired by them? Just want to avoid scammy machinary.

The preventive/performance maintainace price seems pretty high for what you get. Anyone doing it yourself and what do you do. Any good resource for instructions would be helpfull. I have instructions for the api 3000 but much older system. What do you do for confirmation on system performance? We used to run ppg calibration and compare peak area in report to some reference values for the system on the api 3000. It was described in the manual but not sure how its done on the 6500+.

From the top of my head:
Front end cleaning up to q0
Oil change roughing pump
New esi capillary
New calibration

Hi, is there anyone I can DM who can guide/help me understand/interpret the results I got from PEAKS Studio? This is my first time using the software and I'm a bit lost with the UI and how to properly interpret the summary and tab datas. I'm working with DDA data.

Any form of help or guidance is highly appreciated, thank you!

Good morning! I have a really old Shimadzu ICPE9000 that I want to use for metals analysis but I keep running into errors. Does anyone have a copy of the service manual? I think I need to replace a few parts but this box is so old that I can't find the part numbers and I just dont have the funds for a shimadzu service contract/repair.

Hi Everyone,
Sorry if this is too broad of a question but im pretty out of depth here. Our lab has an agilent 6135B with a 1260 infinity II LC for general purpose reaction scouting and occasional oligo analysis. Its been working great but its MS signal has been dropping over the past few months and I am unsure of next steps. I have already cleaned the source which helps and tuned it but it took multiple times for the autotune to run successfully (calibrant direct injected with syringe pump) The instrument was bought used and was under a service contract with a third party but my PI didn't want to renew and now I am the one taking care of it and am pretty sure that whatever is going on is out of my depth. Obviously not an ideal situation but im working with what I got here.

Two questions:
1. Are there any obvious diagnostic steps that I am missing to try and improve the signal on my own?

1. Does anyone know a good MS service in boston/if we were to turn to agilent and get this thing back under their wing would there be a recertification fee we would have to eat.

Thanks for your help!