If you are thinking about building a proteomics laboratory or environment, or writing your proposal, you will probably want to focus all your efforts from and put as a low budget priority the approach of identifying proteins by two-dimensional gel electrophoresis and MALDI MS of peptides extracted from in-gel digestion. It's labor-intensive, and often the percentage of good results do not live up to expectations. At one meeting I attended, one speaker who made use of a proteomics expert in his study told me that his expert does not even bother with 2DGE-MALDI MS-based identifications. He devotes his time completely to LC-MS/MS work, probably using stable isotope labeling for when he wants to get quantitative. We are just sort of starting out doing expression proteomics work and wanted to direct a great deal of effort to 2DGE-MALDI MS approaches to "high throughput" protein identification. After actually doing it, I can see how one can sour on the idea of using 2DGE-MALDI MS. It is attractive initially, since getting 2D gels to look good takes a shorter amount of time, and the use of large gels and narrower pI range strips gives one the illusion of protein purity in a single spot. But with and after the gel excision, things can get complicated. First there is the robotic spot cutter we use. Without our particular robotics spot cutter, just sitting there for any length of time, it can lose its spatial calibration for reasons only Bio-Rad knows. Calibration is also complicated and involved and expensive: it seems we went through a half dozen large sheets of PVDF (yes!) to get the instrument calibrated at one time (moreover the camera was not properly placed). Although not given as an instruction by Bio-Rad, prior to any spot cutting task, the user is well-advised to keep and use scrap gels to test the spatial calibration of the cutter. Before we realized this difficulty, we had lost one set of valuable gels because of wrong assumptions involving the spatial calibration. As necessary controls for the cutting and in-gel digestion process, one must ALWAYS include control proteins (one whose identity is certain) cut from the gels. Naturally we use the molecular weight markers used for the second dimension. We designate manual cutting of several spots: from a single band we cut one spot, and then from the same band 3 or 5 spots, to gauge the sensitivity of the process. Then we go to the in-gel trypsin digestion. We have a MassPREP liquid handling station that also works better in theory than in practice. The thing is supposed to run overnight while the scientist is away, but even after the deck calibration, the tip and lid pickup tests, and other preparations, it seems something ALWAYS goes wrong with it. So we have abandoned the overnight all-in-one process and divided digestion into 2 parts in 2 days, done while the scientist is on duty/at work, to make sure the method moves along. The first part does the reductive alkylation up to the drying of the gel prior to trypsin addition. The 2nd part is the addition of trypsin all the way through to extraction. Why don't we do this manually instead of using the MassPREP? Because, as error-prone as the MassPREP is, whenever a human is involved in pipetting solutions to massive numbers of wells on two or more multi-well plates, the likelihood of error or well contamination by keratins is greater. And so we try to automate as much as possible. One of our problems in the laboratory in which we work is consumables availability and delivery. We work in an environment where money is more valuable than time---which probably means we should not be operating a proteomics laboratory in the first place!! For instance, the people who bought the MassPREP did not buy the MALDI spotting option, and no one ordered ZipTips---which EVERYONE seems to be using---because of the expense. Yes, we have no idea how much ZipTips improve the MALDI signal because of the tight-fistedness of operations around here. So after the in-gel peptide extraction is done, we go to MALDI spotting by hand. Because this is a human activity, one has to be on their toes. I have described a method where the technician does not try to spot the whole plate in one sitting. We first transfer the extracted peptides in their entire volume to narrow conical multiwell plates (MassPREP recommends ABgene 080 plates, and that is smart). We then dry this down with the vacuum centrifuge (SpeedVac). We are then ready to spot. As a standard solvent, we use 50% MeCN + 0.1% TFA. The technician adds about 2.5-3.0 ul of the solvent to the top of the well, and only to ONE COLUMN of wells at a time (8 wells), because the 2.5-3.0 ul can evaporate quickly. The tech does a quick spin in the SpeedVac (because it has a plate carrier) to bring the solvent down to the bottom of the conical well. The matrix (we used saturated or >20 mg/ml CHCA in the 50% MeCN + 0.1% TFA solvent) is then spotted to the MALDI target plate: the Gilson P2 pipet with proper tip is set to about 0.8-0.9 ul. Without changing tips used to spot matrix, we immediately go into the well, use the tip to stir circularly in the well, and pipet up and down a few times, and then take a sample out of the well and pipet it into the matrix bubble already on the plate. We do not even bother to pipet up and down in a mixing action, as we probably lose matrix and protein into the tip anyway. The matrix seems to crystallize and form a nice bed. I advised people to do a spectral acquisition first on that spotting, then if they want to do a relayering with EtOH or MeCN, or use one of the cold-water washing techniques to improve signal-to-noise, they do that after the first run acquisition. As an alternative to manual spotting, I tried to automate the MALDI spotting (albeit without ZipTip enrichment) by setting the 96-multiwell plate in an LC Packings autosampler connected to an LC Packings Probot MALDI spotting tool, but I could not get LC Packings to cooperate with me to get the software to work correctly. The autosampler is run by the Chromeleon software, and the Probot is operated by a separate piece of software called Microcarrier, and the user interface for both programs makes MathCAD understandable to a 6-year old. LC Packings was not very interested in the concept, since they probably thought it bizarre that people would try to use their autosampler/Probot to do MALDI spotting; more shortsightedness here. Finally we get to the spectral acquisition. We use the Waters/Micromass M@LDI-LR, an obsolete piece of equipment. I have already gone on about the problems with MassLynx software used to control the instrument, and to acquire the spectrum, hopefully with accurate masses. MassLynx is bug-free (not really) compared to the bioinformatics nightmare that Waters/Micromass offers to analyze the MALDI data and do protein identifications, ProteinLynx Global Server. I cannot say enough bad things about PLGS, although I have already said plenty. Waters/Micromass has not responded or replied to my laundry list of things that are wrong with PLGS, and why no one should ever waste their valuable time using it, even if it was handed to them without cost (for the cost would be your time!). They continue to believe in the usefulness of their product, although I have put out a call to anyone who claims to use it with good results. ==== Now I suppose that no one really said that expression proteomics work was the proverbial walk in the park. But tell me that my impressions of what is presented in the literature are wrong. Go to any proteomics journal, or an article in which proteomics was used as a tool to answer a question, and there is probably a multi-page table with a list of 250-300 proteins reportedly identified, maybe with a figure of well annotated gel (or gel detail) annotating the spot. Have the authors stated something like, "we detected 800 spots on the gel, cut out 500 of them, went to MALDI and identified 450 of them." What is that? A 90% identification rate of excised spots? Did they even report the score and/or confidence level/probability of identification? Be cautious about that! I believe some are reporting the top-scoring hit off of MASCOT or whatever they are using, and not bothering to tell you if it is indeed a high probability of identification. I just want to warn you out there that if you are planning on using proteomics as a "tool," then do not get the impression that this "tool" is the least of your worries and frustrations doing your research. It's really amazing actually that many laboratories are offering the many techniques of proteomics as a "service." For instance, if I have a 2D gel with 90 proteins I have designated for cutting and identification, and I deliver the gel to the proteomics "service" laboratory, do you not expect to see 90 high quality MALDI spectra with 90 high confidence protein identifications in the report handed to you??? Or at least say 3 in 4, say about 75 of them. Right? What if you got a report back that said, we got 35 high quality MALDI spectra and only 15 identifications? What would say to that? Would you say that proteomics as a tool has fully matured? Come into prime time? Would you call it "high throughput"? Or rather "high throughput in your dreams!"? If anyone has actually paid for a proteomics service and been pleased with the results, I invite them to respond to this post with the actual numbers, the hard data. I want to see for myself just how "high throughput" it is. --- SMH ____________________________________________________________________________________ Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html