- by /u/Solid_Anxiety_4728Hi everyone, I am getting into a new lab where people never did proteomics before. I want to set up a workflow for sample praparation. Everything is find excep the lyophilization. They don't have a speedvac instead there is a Labconco FreeZone 1 Liter Benchtop Freeze Dry System. From my understanding, the noly difference is it doesn't spin the samples. Could samples splatter without spinning, leading to loss or difficult reconstitution? Has anyone successfully used this type of freeze dryer for proteomic samples? Any protocol tips? Thanks in advance. submitted by /u/Solid_Anxiety_4728 [link] [comments]
- by /u/HaushCan anyone offer any tips for doing proteomics on FACS isolated cells? I’ll be sorting low-ish numbers of human leukocyte populations (~50-100k) and I’m wondering what people find are the best methods to minimise cell loss. What do you sort into? Can you lyse directly from the sorted cells without washing? I tried washing ~200k monocytes and T cells in PBS but lost a lot of cells, so I wonder if there are ways to avoid washing steps. I've looked in the literature but couldn't find any papers that go into detail with what I'm looking for. Any help would […]
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experimentsby /u/BioGeek​I'm excited to share our newly published paper, "InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments," now available in Nature Machine Intelligence. In this work, we introduce InstaNovo, a transformer-based neural network designed for de novo peptide sequencing. Trained on 28 million labeled spectra, InstaNovo translates fragment ion peaks from mass spectrometry data into peptide sequences with unprecedented precision, outperforming current state-of-the-art methods on benchmark datasets. Building upon InstaNovo, we developed InstaNovo+, a multinomial diffusion model inspired by human intuition. InstaNovo+ iteratively refines predicted sequences, further enhancing accuracy and reducing false discovery rates. This dual approach combines […]
- by /u/Specialist_Plenty_88Hi, proteomics people! I've been working with DDA for a long time, and now I'm starting to analyze DIA-generated datasets—they are so much more complex! My question is: I have this huge list of 10,000 proteins, and to get a broad overview using tools like heatmaps and PCA, I can't have duplicate proteins… but I do. For the sake of visualization, I simply deleted them since there were only 98. Has anyone encountered this issue before? What would be the best approach? Ideally, the least biased one. Should I just delete them randomly? submitted by /u/Specialist_Plenty_88 [link] [comments]
- by /u/Fit-Slip313From what I can see, there’s 3 alpha-helices, 2 short B-strands that form a short antiparallel B-sheet. I also see a Beta-alpha-beta supersecondary motif which are likely stabilized by VDW interactions between the hydrophobic residues at the crossover point. I also see some loops. I was wondering if there are any turns, I see some areas where sharp changes in direction but I’m not sure if those are turns or not, can anyone help? Also can anyone let me know if I’m missing anything / said something wrong. Thanks! submitted by /u/Fit-Slip313 [link] [comments]
- by /u/Goku101112I am undergraduate student working on my project, in which I am extracting protein from Spirulina. I need help in determining the amino acid profile of the protein. I have an LC-MS report of my protein sample, but I don’t know how to calculate the amino acid profile from the peaks given. I just need an approximate evaluation of the amino acid profile. submitted by /u/Goku101112 [link] [comments]
- by /u/InfinityScientistHi. I'm trying to write a sci-fi story where an evil nutritionist creates a protein in the lab that they intend to release into a city's water supply so it will spread to all the people in a specific area. The protein would be beneficial for health in the short-term, but insidiously in the long term, it would give people who had it a 95% chance of developing cancer or heart disease. I don't want it to be a boring virus, since I want the change to be very slow and not immediate. My questions are 1.) Can proteins be […]
- by /u/AuslanderInMunchenI have a question for people who use Perseus, I want to create a heat map of the median values of 3 matrices. These 3 matrices are replicates and in the end I want a single matrix with median values that I can plot as a heat map in perseus. I have tried merging them and doing summary rows > median, but this creates a separate column which cannot be plotted in the heat map. I would appreciate if anyone could tell me which merge option to use and how to plot the heat map. submitted by /u/AuslanderInMunchen [link] [comments]
- by /u/nitsujdleifHi all. I've collected data for three different cell types on a Bruker QTOF and am looking to compare protein abundance between the three. Is there a metric in TPP that can be used? I know that "Quantic" actually refers to when the instrument picks the peak and not at the peptide's maximum intensity, so I'm weary of using this measure. How is Quantic_TIC different? I've tried to find resources online the explain the different columns but no cigar. Any help is appreciated! submitted by /u/nitsujdleif [link] [comments]
- by /u/BusinessStandard7257Hi everyone,I am comparing results that I get from doing a Tukey's test in Perseus for significantly changing proteins to those I get with an in-house script. They both agree in terms of significant sample pairs but I am not sure what are the values being reported in the "Main" columns for each of my samples in Perseus. I thought they were the mean differences between samples but they are not and sometimes Perseus also reports "0" values in these columns….If anyone has any idea, please let me know. submitted by /u/BusinessStandard7257 [link] [comments]
- by /u/nitsujdleifHi all, I'm new to proteomics (BSc honors student), and I'm trying to look at some mass spectra acquired on a Bruker QTOF that generates profile spectra in the .d file format. I've tried uploading these files directly and converting them to mzML using proteowizard and TPP MSconvert, but nothing seems to be working. Does anyone have experience working with Bruker .d files in MaxQuant? Any advice on file conversions/parameters? Thanks! submitted by /u/nitsujdleif [link] [comments]
- by /u/bluemooninvestorIf a peptide gets phosphorylated, does the mass only increase, or the charge also goes doesn't by 1? Or does it exist in a equilibrium of sorts. Like some peptides have extra – 1 charge while others are unaffected? I am asking specifically for ESI mode. submitted by /u/bluemooninvestor [link] [comments]
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