- by /u/Expensive-Painter-18Has any1 tried using DIA NN for Proteomics ruler based copy number estimation? I know orginal paper is based on MaxQuant and Perseus based plugin but in general, DIA data should be more quantitative and less susceptible to missing values/peptides hence though to use Proteomics ruler concept here. Also, label free quantitation should accurate in DIA mode. Any suggestions/comments? Is my logic right? submitted by /u/Expensive-Painter-18 [link] [comments]
- by /u/Dizzy-Fisherman-7858Hi! This is my first time working with outputs from ProteinLynx Global Server (PLGS), and I would really appreciate some guidance from those who have experience with it. We are using DIA data generated by either the Xevo X2 or X3. The software provides fold change and p-values for each experimental comparison, as well as individual files for each sample. I recently joined the lab and until now people here have been using only the comparison table between conditions provided by PLGS. However, this doesn't allow to go further and plot PCA, Heatmaps and all the classic stuff. I have […]
- by /u/fnepo18Hello! I am working with longitudinal peptidomics data and would appreciate some advice on the most appropriate statistical approach. I have previously worked with standard differential expression analysis, but not in a setting with repeated measurements across multiple timepoints, so I am unsure about the best way to handle this. My dataset contains proteomic measurements from patients belonging to two clinical groups (Disease vs not), measured at multiple timepoints (for example H0, H24, H48). My main goal is to identify proteins that are differentially expressed between the two conditions. My current idea is to fit, for each protein, a linear […]
- by /u/Crazy-Tax-1320Hi everyone, I’m trying to improve peptide/protein recovery after acetone precipitation and was hoping to get some advice. Right now my recovery is inconsistent..most of the times 57%, but it can drop to 47% or even 30%. My workflow: Acetone precipitation (6x volume, 24hrs in -20, 24hrs because I want to start Trypsin digestion at around 4 or 5PM ) Decant supernatant Air dry pellet at 37°C in Incubator for 15–20 min (not longer) Resuspend in TEAB and try to break pellet by pipetting up and down Add trypsin (parafilm as well) and digest overnight (not longer than 16hrs at […]
- by /u/Ok-Piglet-7053Hey r/proteomics, I wanted to share something we've been working on for the past few months that might be useful if you're running Spectronaut analysis on large-scale experiments. The Problem: Conventional Spectronaut workflows process sample sequentially on a single compute node, which works fine at extremely limited scale and becomes a critical throughput bottleneck for large-scale studies. What We Built: An out-of-the-box, cloud-native WDL workflow that distributes Spectronaut DIA analysis across multiple virtual machines on Google Cloud Platform (GCP) via Terra—a computational platform developed by the Broad Institute of MIT and Harvard in collaboration with Microsoft and Verily. This workflow […]
- by /u/EvosepBioHi everyone, We’d like to share an upcoming webinar that may be of interest to the community here! This session is designed to be useful both for experienced users and for those exploring scalable proteomics workflows. On March 24, 2026 (16:00 CET / 11:00 EDT / 08:00 PT), we are hosting another webinar: Scalable Workflows for Standardized Proteomics Speakers: Salla Keskitalo, PhD (LSRI Director, Viikki Proteomics Unit, University of Helsinki) — “Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics.” Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states, and […]
- by /u/thickestbrickestHey all, Master's student here, trying to get my final samples analyzed so I can write up. Before mid-December, I have used FragPipe in the past on my work computer without issue. Sure, it's been slow, but it worked well when I used it in September to analyze some preliminary samples. Using a Thermo Orbitrap Fusion for DDA. I've got 16GB ram to work with but it's consistently thrown an error after the initial MSFragger search. It says it has insufficient memory and stops the program. I reported the error (in case it is one) and the response was basically […]
- by /u/Crazy-Tax-1320Hey everyone, I’m trying to do on bead TMT labeling (following the Udeshi group workflow), but my labeling efficiency is basically failing. I’m getting almost no TMT-labeled peptides, and my IP results are also very poor. IP is being done using PTM scan Ubiqutiin antibodies Here’s what I’m doing: Starting material: 0.5 mg peptides I do antibody incubation with peptides for 2 hours Then wash beads with PBS and TEAB Resuspend beads in TEAB Add TMT (0.4 mg, TMT11) TMT prep: Each vial has 250 ug TMT I add 50 ul ACN to dissolve each vial Combine two vials → […]
- by /u/No-Highlight-9452Hi all, I’m trying to identify phosphohistidine (pHis) sites using MaxQuant, and I defined a custom PTM as follows: Modification settings Type: Standard Composition: H O(3) P Position: Anywhere Specificities STYH STY: copied from the default phospho (STY) settings H: Neutral losses: HO3P, H3O4P, H5O5P Diagnostic peak: H8C5O3PN3 (pHis immonium ion) Previously, using the same raw file, I was able to detect a known pHis site (PtsI H189). However, after switching to a new computer and reinstalling MaxQuant, the same raw file no longer produces the pHis site. To troubleshoot, I ran a few tests with different PTM settings: STYH […]
- by /u/Crazy-Tax-1320Hello everyone! I'm new to DIA. Our lab has been using DDA for a long time, but my PI has decided to try the DIA method. I'm currently reading papers and looking online to learn more about it. One challenge I see is creating a library, since we are limited in starting material like cells and reagents like trypsin. I learned about FragPipe and DIA-NN, which are library-free. Which one do you think is better? since I'm a master’s student and very new to DIA, do you think this is a good project for me to take on? Could someone […]
- by /u/Exotic-Resident127I have a protein complex comprising of about 6-8 proteins, want to map out interaction residues and maybe overlay the findings onto an AF predicted model. Bought the BS3 linker but it's non cleaveable and may not be ideal for my purposes ? Don't know if I should get another linker instead ,please advise ; also how do I do downstream analysis? my MS core uses MaxQuant for everything; I think MaxQuant has MaxLynx for crosslinking analysis but is it the best? has anyone tried out other tools? submitted by /u/Exotic-Resident127 [link] [comments]
- by /u/oatlover666Hello! Is there a way in Perseus to create a volcano plot (or a t-test) that is correcting for a confounding variable, in my case Age? In lipidomics and metabolomics I do this in R: factorial_de submitted by
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