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Johnny Truant posted:Yeah I'm wondering why we're using Na/Na instead of K/Na. Definitely gonna bring it up with my supervisor. I could maybe see some explanation if we were looking at potassium pumps/channels in neurons, but... we're not, haha. Maybe I can point it out and look good to my supervisor PBS is kinda of a lovely buffer, unless of course you are working with cells and have to care about some potassium/sodium balance. Na+ is a stronger ion electrostatically than K+ and considering the amount of Na+ is much higher than the K+, Na+ will dominate the electrostatics. Not doing cell work, but unless my protocol for some reason demands it (we do a lot of stuff on following published protein expression and purification protocols), I would go with either just NaPO4 + NaCl and adjust pH or use something like MES, HEPES, MOPS or Tris. Phospate falls out of solution with Ca and other cations, which cause a lot of issues for us.
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Jul 25, 2016 17:44
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Ezekiel_980 posted:Question for anyone in this thread with a phd, is it still worth getting one anymore? this past weekend i was catching up with a buddy at a local university working on one in the same general field as myself (NMR spectroscopy) the work is really interesting (looking at cell expression via NMR), he said that if i wanted to join the group, because of the level of experience I have (5 years in industry (dear god its been that long...)) his adviser would likely fall over himself trying to get me to join his research group. its tempting since usually you need an phd to work in NMR but i keep hearing about how their are way too many phds and don't want to spend the rest of my life justifying my existence, also having to take a break from money is a bit scary. Typically you still need a PhD to work with NMR, since that is usually the only way you get hands-on experience with spectrometers. Actual NMR work is not really that hard, since most people work on a phenomlogical/black box level with NMR. Cell expression using NMR, are we talking about metabolomics? Cause that is the new hotness within the NMR field. Whether it will lead to actual real jobs outside of the university remains to be seen.
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Aug 1, 2016 12:50
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Ezekiel_980 posted:Currently an analytical chemist specializing in NMR in GMP now. its a ok job at a CRO that I've done it for about 5 years now that started paying pretty well recently. We had a bizarre reshuffle recently where they axed some managers and the most recent hires and now we report to off site managers. Based on how things are looking I will probably have to find a new job in the next year or two. I'm just trying to decide what I might do next, new job in science, double down on science or get the gently caress out of science. As someone with an PhD + postdoc experience in NMR spectroscopy (specifically protein NMR) I would say getting the gently caress out of science is a good idea. The problem is never getting a PhD and then a post doc, it is rather what to do afterwards. Either you go back to industry with rougly the same prospects as you have now (since there are not that many NMR positions out there) or you go on with academia which is a pain of its own. If I am guessing right, the advisor you are talking about does NMR on metabolomics. I know some NMR people that works partly within that field and sofar it seems like a field that is pretty far off from being mature (which of course also is an oppurtunity). Out of sheer NMR curiosity, how do you use NMR in GMP? Looking for impurities using 1D 1H and 13C NMR spectra?
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Aug 2, 2016 05:50
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Ezekiel_980 posted:So I'm gearing up to start sending out my resume, I have a MS and 5 years of experience in pharma hell but it's all in NMR which is utterly useless. How difficult would it be to transition to a position with some sort of growth potential like HPLC or MS with a different organization? Any ideas for how to approach this? What type of NMR? Small-molecule or bigger things? There is a push towards biosimilars in the pharma field and NMR is one part of characterising larger constructs, along with every other biophysical technique you can think of. I know Principal Scientists with a background in protein NMR working on biosimilars both at Pfizer and Amgen.
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Dec 7, 2016 08:26
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Ezekiel_980 posted:Small molecule, at this point I just want to get out of NMR entirely. As interesting as the technique is its a pretty dead end path if you don't have a Ph.D. and I refuse to do any further college since I found the return on investment for my current degrees was not very impressive. Fair enough and true as well. I can tell you from personal experience that even with a PhD in NMR, it is pretty much a dead end path.
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Dec 7, 2016 14:47
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john ashpool posted:Mass Spec 4 lyfe What i have seen of proteomics have left me kinda unimpressed, and I have shared research institution with coworkers of Mannfred Mann. Speaking from a biophysical point of view there are a lot of results in cell biology and proteomics that can't be verified once you isolate the system. We often see it at the company when customers approach us with compounds that have only showed effect in cell assays. As for MS, in some areas like hydrogen exchange, MS is like 20 years behind NMR.
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Jan 14, 2017 07:13
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Appachai posted:As someone who used to work for emerald bio, I respectfully disagree. Didn't they turn into Beryllium, who just got bought up by some pharmaceutical company? In that case, we are in the same field and yeah, don't let the customers know everything.
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Jul 12, 2017 06:12
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Appachai posted:Well, they changed their names several times, went through a bankruptcy( to become beryllium), and then their biggest customer saved them from shutting their doors by buying them...or so I hear. My boss was kinda happy about it since our biggest competitor in Boston is gone now. But he never said anything about financial difficulties at Beryllium.
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Jul 12, 2017 06:56
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Appachai posted:Back when I worked there I used to get collection calls from lab supply vendors on my work number. HarkerBio is going to take over the cro x-ray business (imo) There is a bunch of competitors within that business are and as far as I know Harker are smaller than Proteros. Smart people at Harkers, but they are subsidized by Buffalo University as far as I know.
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Jul 14, 2017 14:05
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Lyon posted:If anyone wants to know more about (or buy How do they deal with various types of data format as in everything from genes to protein structure determination? How easy is it to copy to and from the LIMS and is it fully Mac compatible? Is the pricing fixed or based on number of users? We have one ELN at the company, but it is rather restricted for what we do. We are mainly doing R&D and not QA.
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Jul 21, 2017 21:02
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) LIMS/ELN/LES, this is my annual reminder to the thread that I work for one of the "tier 1" LIMS vendors.
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Youth Decay posted:gently caress Tecan Evo robots, seriously. Supposed to let us run more assays more accurately but they mostly create very expensive headaches. Like what? Ours works rather well, but is mostly used for pipetting crystallization screens and DSF plates.
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Nov 7, 2017 17:58
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Shrieking Muppet posted:My boss has ordered me to attend a data integrity seminar being given by Agilent for the HPLC groups, I work in a dedicated NMR group... He is aware that Agilent killed their NMR business (old Varian)?
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Jan 30, 2018 17:50
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Shrieking Muppet posted:Yes but more importantly we use Bruker Then even more Lol. Typically bosses should be kept away from NMR spectrometers. Are you in small molecule NMR?
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Jan 30, 2018 18:46
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The best equipment I ever worked with was an old Varian UV/Vis spectrometer. All manual levers, but apparently excellent optics. Best thing, half of the times when you put in a cuvette it got stuck at -0.1, which you fixed by giving it a slap at the side. Immensely satisfying.
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Mar 22, 2018 15:20
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Mustached Demon posted:poo poo dude I thought we were bad with keeping 2-3 generations worth of obsolete equipment in every storage space. Well, obviously your boss isn’t a hoarder of old equipment like mine. Ask me about VR googles from the 90s.
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Dec 5, 2018 06:37
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Shrieking Muppet posted:I used a Varian Inova 300 MHz NMR when i was in school from 1993 when i was in school in 2010. it wasn't until the year after i left grad school that it started to break down. Console or magnet? The latter is as it should be, I know a bunch of NMR spectrometers that have been running without quenching since the middle of the 90s. Consoles is another thing though, although if you don’t push the system I guess it could last a long time. The abortion that is Vnmr is another thing though.
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Dec 5, 2018 17:46
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Shrieking Muppet posted:Both, magnet had the seals go bad in 2000 but after that all as well. For 90s software it wasn't that bad to use however when i started working and go to try topspin 2.1 holy gently caress the quality of life was better. The version prior to topspin (xwinnmr?) was pretty horrible though. Also for some reason, whenever I try to run on a 900/950, the fucker quenches and hello a couple of months downtime. Ever since Bruker got a defacto monopoly on the spectrometer business (unless you count JEOL), the speed in doing repairs have gone down. Also, for some reason VNMRJ is now open source if you really want your Varian fix.
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Dec 7, 2018 18:04
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stimulated emission posted:Does anyone else get struck with intrusive thoughts on how you should just take a BIG OL SWIG of whatever you are working with? Looks at ecoli culture and lysate. eh, no.
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Jan 11, 2019 20:11
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Tunicate posted:Wonder how well it'd fight against that protein in miracleberries/ Monellin? I know of an article where the coauthors (professors, post docs and PhDs )willingly tested different mutants of it by ingesting it. One way to get around the ethics committee. Artonos posted:If we're talking accidentally smelling stuff. I got a nice whiff of chloroform once. It burned the nostrils pretty bad and was a pretty small amount. Accidentally smelling stuff is kinda normal procedure. For various reasons we set pH using non diluted HCl which is a constant source of enjoyment.
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Jan 12, 2019 04:52
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Shrieking Muppet posted:I will confess that I've always wanted to taste deuterated water Tastes like water I would assume. Must have tasted it one time or another. Difference between deuterated water and normal water is hydrogen bond strength and molecular weight. Having grown Ecoli in 50% deuterated water the main difference is that everything goes slower but not much else. Also, if you don’t have 20% and 70% solutions of non denatured ethanol standing around everywhere in the lab I don’t know what to say. Helps that we don’t have students and phds in the lab. Lab ethanol kinda loses its charm after having it freely available.
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Jan 12, 2019 18:20
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vivisectvnv posted:you will not find me takin a casual wiff of BME...TEMED on the other hand I kinda like the smell of BME since it was the standard reducing agent during my PhD. Nothing like exposing an entire lab section to this. Nowadays I just judge my ecoli production based on the smell of the lysed cells.
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Jan 13, 2019 07:23
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ascii genitals posted:Agilent also tends to train people too fast and on too much, but they're trying to improve that. It depends a lot on your local management. If they are smart they will send you to training and then do a good amount of mentoring before just throwing you out there. You've always got support, it can just seem like you're on your own. On something else, what molecule is that on your avatar. I see a peptide bond but then something completely else.
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May 27, 2019 07:23
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Ah, yeah. Taxol, the archetypical complex biological molecule.
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May 29, 2019 23:05
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What type of autistic moron came up with the SMARTS query syntax? I just want to look through our fragment library in an easy manner using KNIME and not learn a new crazy language.
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Jun 13, 2019 17:38
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street doc posted:Management sees non-PhD lab work as mundane, and therefor prefers to automate, outsource, or just train someone from scratch. Isn't that kinda stupid since a good research engineer will regularly be better than someone with a PhD? At least that is my experience.
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Sep 5, 2019 14:22
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Since there seem to be a lot of HPLC people around here, I am wondering whether anyone have good recommendations for a HPLC-MS system. Chromatographically there are no heavy requirements, since currently we are running this fine on 10-20 year old LC-MS systems, as well as on a new Sciex system. What we are mostly looking for is supporting software that allows for keeping track of 25-50 compounds in a mix and highly automatized and stable analysis of weak and broad peaks. The system is supposed to run 1000-10000 compounds in mixes. Also, since there are ELN sellers here, anyone got a recommendation for a good one that is customisable to cover anything from cell expressions to protein crystallization and NMR. Preferably self-hosted on our network and must be Mac-friendly.
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Oct 11, 2019 07:40
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Dik Hz posted:Why do you need big files for crystallization data? You don't need to store the image files, do you? Just the reflections.db We store all image files since we never know when we need to go back for reprocessing. Currently we have one project from 2014 that is going to the PDB database and which needed reprocessing. The Eiger detectors that are becoming standard on all big beam lines also create large amounts of data. I will check out the Biovia, the max upload I don’t see as a problem as we would probably keep actual image files separate.
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Oct 12, 2019 10:40
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Dik Hz posted:I get the impulse, but aren't your image files already processed to the pixel anyway? Might be, I only cheat at crystallography and X-ray. My coworkers process from image files using different software for isotropic and anisotropic data so we need the image files. As storage space is cheap and my coworkers have no interest in sorting the data, this is currently the working solution.
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Oct 12, 2019 14:50
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Tunicate posted:Raw image files add up fast, i do optical imaging with a canon camera on a scope, and it's 300-400 MB per 10 second experiment A normal 4 h session at a beamline generates on average something like 500 Gb data, mostly images. Funny fact, nowadays the sample changer takes longer than the actual data collection. That is of course on a good beamline.
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Oct 12, 2019 18:59
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ascii genitals posted:I don't do a lot of lcms but ab sciex ms with an Agilent lc seems like what you are looking for. Just spent the afternoon with a LC MS operator on a Sciex MS and the interface was very much clicking with the mouse, which gets old fast with 1000+ compounds. Anyone here got experience with setting up automated analysis on a Sciex that can point me to some good starting point for that?
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Oct 16, 2019 17:19
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ascii genitals posted:What part are you trying to automate? Same analytical method with different compounds, trying to automate the identification? Same compounds different concentrations? I basically need a way to handle 1000-10000 different known compounds that come in mixes of 25-50 without having to do manual copy pastes or analysis. Chromatography or MS is nothing advanced, it is just that analysis software is not designed for this. Ideally I would want to design batch automation and MS methods in text files using Python/whatever and then having some form of automatic analysis for the chromatograms, since it in 90-95% of the times is a single peak. The only thing I actually care about is the retention time and some information on peak shape.
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Oct 23, 2019 17:41
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ascii genitals posted:Generally you can set a data system to spit out integration RT, abundance, and some other information as excel (csv or better yet tsv.) I don't know Analyst software so I don't know how to recommend the exact steps. We are running on both single and triple quads. Our own library is tuned by MRM, while client libraries are not. We know the monoisotopic masses of what we inject and basically want to detect the RT for them. The RT will vary depending on column and the difference between different columns is the interesting value. I guess I will have to go digging into how the text files are formatted to figure out a way.
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Oct 23, 2019 18:33
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Epitope posted:Is the challenge you want to avoid manually defining RTs? Could you just make a method with RT windows spanning the whole run, export, and automate the rest from there? I only know chromatography software, so not sure if that makes sense with MS Pretty much. Chromatography and MS is pretty insistent on having the correct mass at the correct RT, which does not apply in this application. Your idea is something I have already been thinking about so that makes sense. Now to figure out how that works on our machine. Alternatively I was thinking about converting the MS data to an open format and try a OpenMS/KNIME workflow. Edit: now to find out how to go from text file to acquisition method in analyst, cause having to manually create 100 of them is going to be tedious. Creating a batch acquisition is easy. Cardiac fucked around with this message at 17:27 on Oct 24, 2019 |
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Oct 24, 2019 04:34
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Dik Hz posted:Stuff like that. The churn rate on FSEs is so high that jobs come open frequently. Must be traveling that kills it. Got asked about my interest in a sales position for a instrument manufacturer in my field. Cold calling was one thing, but 50-75% travel time killed any interest. As for my chromatography question, I think I have the solutions. Batch list is easy, since it is a text file. New acquisition method for each mix means learning Visual Basic apparently. We are running SIM so the masses are known and the wiff files can be converted using ProteoWizard and read into KNIME/OpenMS for processing.
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Oct 26, 2019 05:10
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Anyone here know whether Agilent provides an interface that allows automatising batch runs and acquisition methods for MS? I know Sciex provides a VB.net that should allow for this. In contrast, Thermos software does not offer this alternative. Googled a bit on Agilent, but no luck. Analysis is less of an issue, as Proteowizard can convert from vendor formats to mzML and the rest can be solved by programming.
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Nov 20, 2019 07:51
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Shrieking Muppet posted:I have a lead at an organization located in the southwest where i want to move too. One thing about them that has me concerned is that they are a start up, from a chemist pov how is working for a pharma start up? I would say heavily dependent on the founder(s). Depending on the size, you will get to do a lot of different things and things can kinda unstructured. We do a lot of work for small and medium-sized US-based pharma companies and the variation in professionality is highly varying.
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Jul 1, 2020 06:49
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Spikes32 posted:My partner is trying to figure out if we can move to Sweden. He'll be able to get me a work visa, but I'm having trouble finding LIMS jobs in the EU. Labware has one job in 'Europe' but I don't have the experience called for. Any suggestions or knowledge of the lims scene a cross the pond? Labware have Swedish employees since I yesterday got an email in Swedish from them. ( we are looking for a new eln). If it has to be Sweden, I would look at the Copenhagen area in Denmark since you have plenty of pharma including Novo Nordisk there and the commute from south of Sweden is like an hour. Plenty of Swedes are working in Denmark and commuting daily.
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Mar 5, 2021 05:01
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Spikes32 posted:Thanks appreciate it. And yeah partners job (which is still just a maybe) would be in Stockholm. He's interning for Erikson and might get an offer post PhD for the kista office. Or maybe San Jose California. I'm rooting for remote / San Jose but trying to do my homework. So Stockholm. You have what remains of AstraZenecas production facilities in Södertälje south of Stockholm, a Pfizer facility making hGH in Strängnäs, what remains of Sobi in Stockholm and maybe Scilife which is university, but aimed at biologicals. Oh and Cytiva in Uppsala (former GE) who produces the FPLCs who are industry standard in protein production. Plus a bunch of small size pharma. Speaking of Erikson, they have a site in south of Sweden in Lund.
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Mar 5, 2021 18:25
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mllaneza posted:If you end up landing in the Bay Area, look into Genentech, we could use more goons. And working here does not suck. We've got something like 800 PathLIMS users, and anyone who wants to write their own ticket for lab automation should be looking in our direction. The new head of research and early development is big on computational biology, so R and Python are both in demand. Out of professional curiosity, how much effort are Genentech putting into using machine leaning/AI for drug discovery?
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Mar 24, 2021 06:24
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I keep getting these scam mails. I am assuming I am not the only one getting these. Anyone knows what the setup is? Example below: Hello, I came across one of your published papers. My company is looking to buy a used Waters Triple Quadrupole Mass Spectrometer and I noticed that you were referring to a similar model in your research, so I thought maybe you would consider selling your old instrument. In particular, we are looking to buy a Waters Xevo TQ-S or TQ-D models. Please let me know if your lab is planning to retire anything. We will be happy to make an offer. Thanks!
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May 22, 2021 20:03
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