- by /u/vihaan29006Hey everyone, I recently built a Google Colab tool to simplify a task that kept eating up a lot of time during my work with bacterial genomes — manually extracting amino acid sequences for a specific set of genes from .gff3 and .fasta files. Introducing GeneAAExtractor 🧬 What it does: Takes a .gff3 + .fasta + gene list .txt file as input Extracts only amino acid sequences for the genes you specify Names each output file in the format: GeneName IsolateName.faa Outputs all extracted sequences in a downloadable .zip Built using: Python + Biopython + Google Colab No dependencies like […]
- by /u/Organic_Nature_939Need to make a lecture about omics analysis and thought I make a tier list based on this meme. I'm not an expert for most of these, so I would appreciate feedback if this makes sense / is accurate:) https://preview.redd.it/girq9hrlyu4f1.png?width=769&format=png&auto=webp&s=02a810512d46b68f29b57986e532e63d5c8fa674 submitted by /u/Organic_Nature_939 [link] [comments]
- by /u/hello_friendssssHello, I am preparing to do some proteomics work on human lung tissue, which is a new one for our group. Has anyone with experience of working with lung tissue got any tips for sample preparation, or protocols/papers they particularly recommend? (I am reading around as well, don't worry) Thanks! submitted by /u/hello_friendssss [link] [comments]
- by /u/Dominos_pizaAccording to the SP3 protocol, it is described as a lossless method. However, during my attempts to assess peptide recovery using BSA protein digestion, I consistently observed recovery rates of only 40–50%. Despite optimizing various parameters outlined in the SP3 protocol, I have been unable to achieve higher recovery rates. Additionally, I’ve noticed a significant lack of reproducibility. When my labmate performs the same procedure using the identical protocol, the recovery rates vary substantially from run to run. My PI is strongly encouraging me to improve both the peptide recovery and the reproducibility of the method using BSA before I […]
- by /u/totallyhuman1234567Hey all I’m trying to wrap my head around the differences between CyTOF (from Standard BioTools) and timsTOF (Bruker). I know one’s mass cytometry and the other’s mass spec, but beyond the basics, I’m curious how they compare in real-world lab use. Where does CyTOF actually shine? Is it still relevant for single-cell analysis or are newer mass spec approaches catching up? And for those who’ve used both what are the tradeoffs in terms of throughput, resolution, cost, usability, etc.? Appreciate any thoughts or experience you can share! submitted by /u/totallyhuman1234567 [link] [comments]
- by /u/Antique-Property-761For those who run timsTOF, do you regularly run system suitability or QC? submitted by /u/Antique-Property-761 [link] [comments]
- by /u/sarcastic_frenchfryHi everyone, I need help with phosphoproteomic data analysis…. is it alright to use the intensity values from the Phospho (STY)Sites.txt generated by MaxQuant for quantitative analysis to determine differentially phosphorylated peptides and use the those flagged phosphopeptides to check intensity__1-__3 (a more qualitative approach). Does normalising the intensity from Phospho (STY)Sites.txt against intensity from Protein Group.txt from the total protein data set make sense? Thank you Really tired student 😀 submitted by /u/sarcastic_frenchfry [link] [comments]
- by /u/Vailhemsubmitted by /u/Vailhem [link] [comments]
- by /u/Logical-Composer9928https://preview.redd.it/ylm1ygspuz1f1.png?width=735&format=png&auto=webp&s=760533670f5f478560decba805b3bb0b0682b30b Hello All, I'm trying to do some Proteome melting assay using the Bioconductor TPP package. We have two sets of 10-plex TMT data ( I & II) obtained as two raw files. I want to search them in Proteome Discoverer 3.0. Shall I search them "By File" which would make two search result files OR shall I uncheck the option which would make one result file with info on intensities for different channels as well as files are provided? From which I can extract TMT Experiment specific ( I & II) data Thanks submitted by /u/Logical-Composer9928 [link] [comments]
- by /u/bluemooninvestorI am running a SPS MS3 method. The MS2 is in ion trap with CID. I have kept 400-1600 as the fixed scan range. I have two questions. (1) Is it better to keep it in "first mass" or "auto" mode? Will that help me get better quantitation? (2) I do not operate the instrument. The scientist in-charge informed me that "first mass" scan mode cannot be implemented with CID? Why is it so? Or is it a software issue? Can the "auto" mode be implemented? Thanks in advance. submitted by /u/bluemooninvestor [link] [comments]
- by /u/Antique-Property-761Is it really unlikely to get N- or -C terminal peptides in a digest of bottom-up proteomics with either orbi or timsTOF? submitted by /u/Antique-Property-761 [link] [comments]
- by /u/Ill_Friendship3057Anyone ever do pseudotime on proteomics data? I asked ChatGPT and it wrote code for using Monocle, but as far as I know that is a tool for scRNAseq. Would Monocle still work? submitted by /u/Ill_Friendship3057 [link] [comments]
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