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IDeA National Resource for Quantitative Proteomics
Приєднався 5 тра 2021
This channel is a repository of videos and how-to guides on topics related to the Proteomics and Bioinformatics related to Proteomics. If you have requests or questions please inquire at IDEAProteomics@uams.edu.
A quick look at using the Spectronaut viewer for DIA projects
Dennis Province, from the IDeA National Resource for Quantitative Proteomics, spends a few minutes explaining how Spectronaut can be used to look at Data Independent Acquisition projects. This free viewer, which can be requested at biognosys.com/software/viewers/ can be used to look at (*.sne) files. Every DIA project from the National Resource will contain one of these files.
Переглядів: 68
Відео
Best practices of managing a core facility
Переглядів 544 місяці тому
This final discussion of the 2024 Core Directors' Symposium focuses on the hot topics of managing a proteomics core facility. Some of the topics include communication and how to head off problems, data management, terms and conditions, sample lists approval before the samples are sent, administration, the benefit of an external advisory committee, etc.
Core Directors' Symposium - What is the biggest challenge to the DIA workflow?
Переглядів 684 місяці тому
This discussion over the lunch asks our attendees the question: What is the biggest challenge to implementing DIA? Aaron Storey from Arkana Labs starts the conversionation and others chime in. Analyzing the data after the data base search, how much is the data validation the burden of the core and how much is the investigator, how can we figure out how each different software package is evaluti...
Core Directors' Symposium - Putting it all together! Thoughts on implementing DIA
Переглядів 524 місяці тому
In this discussion the core directors of the symposium share challenges to implementing DIA. This discussion ranges from the technical challenges to communication with other cores to financial barriers presented by administators. All things that a core director is concerned with is discussed! Task management system Monday.com is also briefly shown and how it can be used to track projects for re...
ProteoDA - a package for quantitative proteomics
Переглядів 1644 місяці тому
Stephanie Byrum goes into the R-script code which allows users to perform their own Bioinformatics on the results from a database search. ProteoDA does QC, normalization and differential analysis. This video describes the code that can be downloaded from her GitHub and run through R-STudio.
Data Collection Experiment - Comparing Spectronaut to DIANN
Переглядів 3124 місяці тому
In this video Dennis Province walks through an set of experiments designed to compare different data collection paraments. One parameter is whether an overlapped or non-overlapped DIA workflow provides a significantly greater number of protein IDs after database searching with DIANN.
Data Collection Methods - An example of how to find the points across the peak in DIA
Переглядів 554 місяці тому
This video shows a short example of how to use Qual Browser to interrogate DIA raw data for a particular peptide. It shows how to identify the number of points across the peak measured for the MS2 quantification. This video also shows output from Spectronaut. Finally, there is a great discussion about how and who evaluates the data, at the spectra level, for a global proteomics experiment.
Technological Advancement in MS, Data Independent Acquisition and Data Analysis - ThermoFisher
Переглядів 1134 місяці тому
In this video, Khatereh Motamedchaboki and David M. Horn from ThermoFisher introduce the Ardia system for storing mass spectrometry data from proteomics experiments. Chimerys is also discussed as well. This "lunch and learn" presentation was part of the Core Directors' Symposium presented by the IDeA National Resource for Quantitative Proteomics.
TINSTAAFL - Instrumentation for DIA - Rick Edmondson
Переглядів 394 місяці тому
In this video Rick Edmondson from the IDeA National Resource for Quantitative Proteomics talks about the different parameters that affect the quality of the data in a DIA experiment. Chromatography is key and the MS parameters must be set to reflect the peak width. Scan speed, size of the DIA window, and the range of the DIA windows can all be adjusted. Rick reminds us that there is no such thi...
Introductions - Core Directors' Symposium - 2024
Переглядів 174 місяці тому
In this video our attendees introduced themselves.
Introduction by Alan Tackett - Day 1
Переглядів 234 місяці тому
This is a short introduction by Alan Tackett to kick off the beginning of the 2024 Core Directors' Symposium held on the campus of UAMS. This Symposium, coordinated and conducted by the IDeA National Resource for Quantitative Proteomics brings together core directors and staff from Proteomics labs across the country.
Phospho-proteomics - Fundamentals of Prtoeomics - Day 2
Переглядів 2085 місяців тому
In this video Rick Edmondson explains some of the challenges of phospho-proteomics. He also talks about the off-line fractionation workflow that is done here at the IDeA National Resource for Quantitative Proteomics.
Graduate and Post-doc Internship plus Voucher Program
Переглядів 755 місяців тому
In this video Dennis Province walks through the graduate/post-doc internship as well as the voucher program at the IDeA National Resource for Quantitative Proteomics.
ProteoDA - How to do your own analysis - Day 2
Переглядів 1775 місяців тому
In this video Stephanie Byrum shows the power of BigOmics, a new, cloud based multiomics tool. She then talks about the code behind the ProteoDA R-code which scientists at the IDeA National Resource for Quantitative Proteomics created. This powerful R package allows output data from database searches (those that come from Spectronaut, DIANN, and Scaffold DIA) to be analyzed. This video will wal...
Group Consult and Questions - Day 1
Переглядів 1115 місяців тому
This discussion centers around the questions that our workshop attendees had concerning their projects. Some of the topics covered in this session included: phospho proteomics, phosphorylated tyrosine, experimental setup for cell culture with multiple cell lines (is it better to run each cell line with their treatments on different days?), normalization at the global level vs at the local level...
Advances in proteomics sample prep reagents and quantitative MS workflows
Переглядів 6285 місяців тому
Advances in proteomics sample prep reagents and quantitative MS workflows
Experimental Design - Exploring Linear Models in Omics Data
Переглядів 965 місяців тому
Experimental Design - Exploring Linear Models in Omics Data
Sample Prep tips - Fundamentals of Proteomics Workshop 2024 - Day 1
Переглядів 2285 місяців тому
Sample Prep tips - Fundamentals of Proteomics Workshop 2024 - Day 1
Fundamentals of Proteomics Workshop 2024 - Overview
Переглядів 4025 місяців тому
Fundamentals of Proteomics Workshop 2024 - Overview
Fundamentals pf Proteomics - Part 2 The properties of peptides
Переглядів 252Рік тому
Fundamentals pf Proteomics - Part 2 The properties of peptides
Offline Fractionation - How and why we combine 46 fractions into 18 Superfractions
Переглядів 105Рік тому
Offline Fractionation - How and why we combine 46 fractions into 18 Superfractions
Experimental Design Suggestions for the Proteomics Voucher Program
Переглядів 383Рік тому
Experimental Design Suggestions for the Proteomics Voucher Program
Tour of Global Proteomics and the National Resource for Quantitative Proteomics
Переглядів 116Рік тому
Tour of Global Proteomics and the National Resource for Quantitative Proteomics
Protein Protein Interactions - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Переглядів 1662 роки тому
Protein Protein Interactions - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Phosphopeptides - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Переглядів 2962 роки тому
Phosphopeptides - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Failed Proteomics Experiments - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Переглядів 1002 роки тому
Failed Proteomics Experiments - Rick Edmondson - IDeA National Resource for Quantitative Proteomics
Experimental Design Sam Mackintosh - IDeA National Resource for Quantitative Proteomics
Переглядів 1012 роки тому
Experimental Design Sam Mackintosh - IDeA National Resource for Quantitative Proteomics
As part of downstream analysis e.g. reactome, I need to use the protein IDs or gene names from my raw data. These downstream analysis dont work when there are multiple IDs per row hence they need to be separated with each protein having its own value. Since there are multiple IDs per row, do you assume that the Reporter intensity corrected value for each protein or gene in a given row is the same?
كيس الظهر
Pretty neat video, it helped me get started with TMT data! Thanks!
Glad it helped!
@@ideanationalresourceforqua4640 I was looking for such a video for setting up MaxQuant for Ligandomics/Immunopeptidomics datasets, is there one available? I couldn't find it.
@@ideanationalresourceforqua4640 I'm wondering if you have such a video for MaxQuant setup for Immunopeptidomics data?
@@ideanationalresourceforqua4640 I've another question, do you use the "Reference channel" column in the experimental design/Raw files window? I'm wondering if this is an optional feature to be used only when multiple sets of TMTn plex are used in a single experiment?
I have been intending to answer this but the short answer is no... if we are doing non-specific digestion we use a program called Peaks. I have not tried this on MaxQuant.
Hi, from where we take the data which we use as a input?
What i would like to know is how to generate that result file. Where can i learn that?
I have forwarded this on to Stephanie. Thanks for your question.
github.com/ByrumLab/proteoDA Here you go.
Thanks@@ideanationalresourceforqua4640
Hi Denis! With 30 processors, approximately how long does it take to complete you MaxQuant runs (per .raw file)? Thanks!
It takes 30-45 minutes for a single ratiocheck raw file. Several hours for a 6 or 10 plex.
In this video, you did not give the fraction numbers in the though there are multiple (18 fractions) fractions. I am curious, was this omitted intentionally? Kindly give insight.
Sorry for the delay to your question. You are correct, this project was offline fractionated and then 18 superfractions were made from the 46 fractions that our 60 minute gradient provides. Each of these 18 superfractions were ran on the Eclipse and the raw files for each of these were then imported into MQ for analysis. Most TMT experiments will have some offline fractionation to increase depth, ours happens to be 18. The file names have the fraction numbers included and the lysates were in a different experiment than the phospho enriched fractions. Does that answer your question? I could provide a video explaining the process of fractionation if anyone is interested.
@@ideanationalresourceforqua4640 Thank you for getting back to me. If you can kindly make a video regarding the fractionation, that would be very helpful. Particularly for bioinformatician who are not confident with the wet lab experimental setup. Thanks!
I am working on this! Thank you for your patience.
ua-cam.com/video/UiWU_zgBlG4/v-deo.html
thanks Mr. Dennis Province. this has helped me a lot.
Looking for how to run MaxQuant analysis on TMT-10-plex fractionated samples [Paper - Archer et al, Medulloblastoma]
@@ideanationalresourceforqua4640 yes sir/madam, i am interested, it would be really helpful. I actually want to run MaxQuant ptm (Phospho (STY)) analysis on the phosphoproteome mass spec raw files.
There is about one minute of blurring during this presentation. It was intentional