- by /u/Proteo-Freak973Hello Folks, I'm interested in applying some machine learning techniques to my Glycoproteomic data (Once generated, Hopefully) simple one, I dont want to keep it as a different chapter, I want to do it as my personal work so even if I fail it doesn't matter a lot. So can someone please suggest what kind of techniques or small algorithm will be helpful for Glycoproteomics data analysis in Plants perspective (e.g. I read somewhere Glyco annotation tools are there similar stuff) submitted by /u/Proteo-Freak973 [link] [comments]
- by /u/Few-Ship-5531Hello (french below), I am a biology PhD student and I have mass spectrometry data to analyze. I started my analysis on Perseus and filtered the data to remove contaminants—inverse and identify only by site. I established my groups with categorical annotation, performed log2 transformation and imputation, and obtained my volcano plot. However, I don't really have an overview of what I need to do next to continue sorting my data. I think I need to do the t-test (which is done automatically with the volcano plot, I think) and the limma test, which should give me information about enrichment, […]
- by /u/Glittering-Card4638Something I don’t understand about the Australian peptide industry is why LC-MS isn’t standard practice across the board. HPLC purity percentage tells part of the story but without mass confirmation, degradation fragments or incorrect sequences could still pass visually as “clean.” In research settings, MS confirmation is non-negotiable. So why are retail peptide markets still leaning heavily on HPLC-only documentation? Are Australian labs: Using calibrated reference standards? Running system suitability testing? Validating methods according to ICH guidelines? Testing for residual solvents? I’ve seen discussions where people send products to independent labs like neurogenresearch for verification. That makes me wonder should […]
- by /u/FactorAgreeable7518Hi everyone, Could someone please guide me on where I can download the Human gut microbial/microbial database (FASTA) file for my proteomics search? I would greatly appreciate it. Thanks! submitted by /u/FactorAgreeable7518 [link] [comments]
- by /u/Proteo-Freak973Hello all, can someone guide me how long does it take to develop a phosphoproteomics workflow by Bottom up DDA approach, what are the major steps involved and thinking model what we can do with phosphoproteomics, goal is to complete within 1 year max and for Glycosylation i want to keep it simple so any suggestions or any research idea will be really appreciated from experienced students and the study is about Plants submitted by /u/Proteo-Freak973 [link] [comments]
- by /u/Most-Marsupial-5366I'm wondering if anyone has tips for getting stubborn peptides to dissolve in 0.1% TFA. They've been digested with LysC, speed vac'd, and now I'm trying to dissolve in TFA so I can proceed with Pierce desalting columns. (cat 89852). But no matter what I do they won't go into solution. The solution is cloudy/milky looking, and after a while of sitting the pellet just settles back to the bottom of the tube. I don't want to send this through the spin columns without it being fully dissolved first. Wondering if anyone has any tips or tricks. edit: Thanks for […]
- by /u/fifedawg11https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2022.995590/full Does anyone have experience with protocols which reliably enrich C-terminal peptides from mammalian cell proteomes?. This is the most recent paper I could find in the topic which used HEK293T cells as a model, which is the cell line I am going to be working with, but I haven't seen this paper cited by any other research groups. Just curious if anyone on this sub has tried this method, or others similar to it, and have any recommendations, warnings, or tweaks to established protocols. Thanks for your help! submitted by /u/fifedawg11 [link] [comments]
- by /u/saintexpress-devHey everyone, I’ve spent a lot of time working with SAINTexpress for protein-protein interaction scoring, and while the tool is industry-standard, I noticed that many of my lab colleagues struggled with the setup and command-line execution. To make it more accessible, I built the SAINTexpress Analysis Portal: https://www.saintexpress.org What it does: – Provides a point-and-click interface for SPC and INT scoring. – Handles the technical "building" and execution on the backend (OCI-powered). – Standardizes input/output without needing to install source code or manage dependencies. Privacy: All data is stored temporarily and purged every 24 hours. Transparency & Open Source: To […]
- by /u/Expensive-Painter-18Need to establish a high throughput proteomics sample prep at my workplace. Can rely on commercial available kits as budget can be adjusted for it. Have tried 96 well Easy prep from Thermo (4 hrs rxn time). Protein numbers are decent around 5-6k in 40 min gradient on ZenoTof. Are there any other options available? Any idea if there is possibility that certain low abundant proteins can be missed by using such kits? Has any1 tried comparing kits for protein recoveries? Please comment. Thanks MD submitted by /u/Expensive-Painter-18 [link] [comments]
- by /u/AncientProteinsI’m opening a new lab, and am interested in adding search program licenses to the funding application. I’ve always used the options available via my local core facility, but that won’t be an option here. Mainly interested in Mascot or PEAKS, or what computing power is needed for MaxQuant (since it’s free). Does anyone have experience with how much these cost? And if it’s a one-time or annual payment? submitted by /u/AncientProteins [link] [comments]
- by /u/FactorAgreeable7518Hi everyone, I’m working on a project to identify microbiota and microbial peptides, but I’m encountering a challenge with tryptic digest samples. My plan is to conduct a “no enzyme” search against a human and microbial database. I’ll then filter out entries annotated in the accession column, excluding those labeled as “human IDs.” (I’ll eventually look at the protein column and work with associated peptides.) My objective is to specifically identify endogenous processed microbiota and microbial peptides. To strengthen my findings, I intend to blast those sequences to determine if they match 100% to any bacterial species. I would greatly […]
- by /u/Thick_Holiday_9180Hi everyone, I hope you are all doing well. I am quite new to proteomics and would be very grateful for your advice on StageTip materials for peptide clean-up. From what I understand, there are three commonly used options: Empore Octadecyl C18-HD disk ( 98-0604-0217-3) SDB-XC disk ( 98-0604-0226-4EA) SDB-RPS disk ( 98-0604-0223-1EA) May I kindly ask which one you would recommend as the best first choice for a workflow involving ABPP probe enrichment, followed by on-bead digestion and then peptide clean-up? If you have any additional practical suggestions or tips for this type of workflow, I would sincerely appreciate […]
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