- by /u/West_Camel_8577In perseus I filtered my matrix to exclude potential contaminants, decoy sequences, and proteins only identified by site. I then log2 transformed the intensity values and they are now all negative numbers. I am not sure if the normalization modes I set in MaxQuant (v2.6.7.0) mean that I shouldn't normalize my data in this way (I was using the Reporter_Intensity columns, not the "corrected" or "counts" reporter intensity) My MaxQuant settings are: TYPE: Reporter MS2, I have entered the correction values for my batch of TMT 10-plex, Filter by PIF is selected -> Min. reporter PIF 0.6 Min. base peak […]
- by /u/Specific-Quiet-8374I'm a PhD student who's field of study has nothing to do with mass spec (and also my advisor doesn't know anything about it either). I collected breath samples as part of a clinical study and then processed the samples by SPME GC-MS. We are specifically wanting to look for VOCs (just putative compound class-level identification) and try to broadly analyze differences between the VOC profile in the patients over time (through disease progression). The prof who's GC-MS system I used does not typically work with this type of data, usually he does insecticides, so he's not much help. I […]
- by /u/31P_GirlWe’ve been working to bring our LCMS back to life for the past six months. We’ve replaced various parts, and both the turbo pump and controller are functioning properly. However, we now need to restore communication to COM1 and COM2. We were advised to try replacing the wires, but an engineer mentioned that we might need a BIOS setup file. Unfortunately, since this machine is outdated, Thermo no longer supports it, and their technical support team is unable to assist. If anyone has advice or access to a BIOS setup file for this machine, your help would be greatly appreciated. […]
- by /u/Logical-Composer9928submitted by /u/Logical-Composer9928 [link] [comments]
- by /u/Internal_Copy_9632Hi everyone. I need to move my ICP-MS Spectro Ametek MSS001 to my new laboratory. I know the optical part needs to be in "service mode" in order to move the instrument without causing any trouble and I'm trying to figure out how to set this mode but I'm stuck. I opened the software (MAV) and clicked on the system window to select the service mode but the instrument is unresponsive. Does anyone have any tip? Do I need to connect the instrument to argon in order to do it? Just asking because we already have disconnected all the gas […]
- by /u/BeehavioralEcologistHello everyone, I am trying to salvage an old-ish project that consists of ~600 samples and trying to find an efficient, low budget (aka no budget) way to identify what's in each sample. I have been using AMDIS, but it has taken a month to do 10 samples, which is obviously not great. Is there a way I can mass process these samples, or is that a no-go using AMDIS? Any information and/or guidance is appreciated here. This is very much outside my field. Thank you in advance 🙂 submitted by /u/BeehavioralEcologist [link] [comments]
- by /u/nintendochemist1Hello! I've finally managed to resurrect our Thermo LTQ. It turned out to be the Digital PCB, haha. However, I'm now encountering issues with calibration. The system passes all steps up to the mass calibration and resolution, and I can see all the peaks. But as soon as it begins the calibration, peak 524 disappears, which is unusual. I’m wondering if this could be contamination from the ultramark in the standard, since I know it tends to stick around. Does anyone have any advice or tips on this issue? I've attached the parameters and spectrum below. Spectrum showing the 524 […]
- by /u/Ambitious-Swan6062Hello everyone! I’m currently working on HS-SPME-GC/MS analysis of essential oils, and I’ve run into a few issues with my blanks that I’d love to get your advice on. ANALYSIS SETUP: I’m using an Agilent 8890 GC system coupled with a 5977B mass spectrometer, with a PAL autosampler and SPME tool. The fiber I’m using is the dark grey (5191-5874), and the column is an Agilent DB-WAX (122-7032), with a temperature range of 20°C-250°C (260°C). The fiber was conditioned for 2 hours at 240°C in the inlet, following the manufacturer’s recommended range (up to 280°C), but I kept it below […]
- by /u/Safe_Problem6038Today I was planning on cleaning the lenses of a tribrid LCMS. Let the instrument cool down for about an hour after breaking vacuum, and pulled out the lenses. Once this was done we found a puddle of oil at the bottom of the lense housing. Found out the condensation on the source window itself was actually oil. Is the instrument forever dead or is there a solution to this? The instrument is under a service contract and we have deemed this to be due to a pump seal or piston failure within the vacuum pump itself. Confirmed oil by […]
- by /u/CwisGunzaHello everyone. Me and someone else are looking into possibly making a mass spectrometer for measuring biomolecules like lipids or proteins. I wonder if something like this could be used, or would another method of mass spectrometry be required? https://youtu.be/nIKhUizkXxA?si=dytGpjvERMUHy0lY If so, what other methods could I use aside from flame ionization detectors, and could this even be done DIY? submitted by /u/CwisGunza [link] [comments]
- by /u/sarahhxmargaretHi all, I know this is technically a mass spec sub but I'm hoping someone can still offer some insight. I work with Agilent LCMS QTOF equipment. We use a Diode Array Detector for UV detection in tandem with our MS. Lately I am seeing a rise in our UV baseline over time. I thought (and still do think) that it is mobile phase related. We use 3 different phases on a gradient (A phase is water with methanol, formic acid, and ammonium hydroxide; B phase is Methanol with Formic, C phase is just IPA) I made new phase, flushed […]
- by /u/bcuriosity90I made a couple calculators to simulate ion motion in a quadrupole on Desmos for fun/trying to understand it more. Let me know what you think. https://www.desmos.com/calculator/pxvenkikbg submitted by /u/bcuriosity90 [link] [comments]
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