- Видео 12
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Environmental Proteomics Lab Tutorials
США
Добавлен 20 апр 2020
This page has information on how the Tomanek Environmental Proteomics Lab runs and analyzes proteins.
Bar graphs with standard error in excel
Here's a quick tutorial on how to make bar graphs with the standard error in excel for more than one treatment group. Excel is better than JMP for customization, and just overall appearance :)
The data I used was some of my normalized proteomics relative abundance data.
The data I used was some of my normalized proteomics relative abundance data.
Просмотров: 1 914
Видео
Gel Electrophoresis and Western Transfer
Просмотров 1894 года назад
This is a video of the Tomanek Lab protocol for the first steps of a western blot.
Quantifying Western Blot gels using BioRad Image Lab 6
Просмотров 28 тыс.4 года назад
This is a tutorial for using the program, Biorad Imagelab 6. Here we explain how to quantify bands relative to a standard protein amount.
Tomanek Lab Workflows for Label Free Quantification of Mussel Proteins
Просмотров 1,1 тыс.4 года назад
This video describes how we analyze our proteomics samples in Proteome Discoverer using the MS Amanda, Spectral Clustering, and ApQuant nodes. The specific parameters used for our study are described.
Overview of Proteome Discoverer
Просмотров 16 тыс.4 года назад
In this video, I talk about setting up a study in Proteome Discoverer to analyze MS data. The video includes an overview of setting study factors, inputting files, tailoring the workflows to needs, and some components of the data generated in the results files.
Analyzing MS chromatograms using QualBrowser
Просмотров 11 тыс.4 года назад
This tutorial shows how to use QualBrowser in XCalibur to look at the data collected for a Full MS and MS/MS run. It includes ways to double check the efficiency the instrument and quality of the runs, as well as how to evaluate your raw data.
Tomanek lab method for shotgun proteomics
Просмотров 4264 года назад
This is an overview of the instrument method used for LC-MS analysis of Mytilus gill proteins using the Q-Exactive Plus. It details the parameters used for separation and fragmentation.
Overview of pre-column setup for LC-MS
Просмотров 8984 года назад
This diagrams the setup and valve configurations for the pre-column (or trap column) setup for the QExactive Plus. Switching the valves from 1_2 to 10_1 alters the flow through the 10-port valve so that sample is loaded onto the trap column and then onto the analytical column.
Overview of the Q Exactive Plus and Ultimate 3000 Instruments
Просмотров 9 тыс.4 года назад
This (awkward) video shows how the Q Exactive Plus LC-MS is configured and explains various components of the LC.
Setting up an instrument method in XCalibur
Просмотров 10 тыс.4 года назад
This shows how to use the Instrument Setup tab in XCalibur (Thermo) to put together an instrument method for automated control of the Q-Exactive Plus LC-MS.
Operating the Ultimate 3000 in XCalibur
Просмотров 6 тыс.4 года назад
This tutorial shows how to control the Ultimate 3000 LC using the XCalibur software from Thermo. This includes setting various parameters of the LC, operating the pumps and flow rates, and basic maintenance procedures.
How to use Tune
Просмотров 8 тыс.4 года назад
This is a tutorial of how to use the Thermo Fisher program Tune to operate the Q Exactive Plus at Cal Poly University. The video is a brief overview of the program for manual operation of the instrument and basic evaluation procedures.
Thank you for the informative tutorial. However, the sound and picture quality are poor.
Hello, I have a question. I want to start a new method. And I have a problem with raw file when I create procesing setup. How can I make a raw file? Can I use the random method in sequence and then this file put in my method?
Its really very helpful. Thank you
I've been playing with this and I'm almost certain that most people don't run a serial dilution of a given sample to validate quantity vs signal or band intensity (area under the curves) vs amount loaded. ie. What does a 20% increase or decrease or increase look like? I played with the exposure/maximum signal before saturation, and I get the best linearity of the antibody signal/quantity when the exposure is only 20-30% of the maximum.
Honestly this is good practice, but undoable in today's conditions. A regular lab doesn't have neither the time nor the ability to keep up with all the controls. I blame the mindset of fast publishing that pushes you to do quantity over quality.
Thank you. This has been so helpful
how do we identify ketone in marine sediments ? Do you have any compound identification list and m/z numbers specifically?? if so can you help me with this?
Please redo so that the full screen can be seen!
when I click the lane profile option, it shows me inverted peaks. How can I dissolve that problem?
Thanks for the video!!! It's very useful!
Hi Melissa, is is possible in xcalibur to use a method with switching polarity, both positive and negative in the same method?
Yes, we can use both in same method
The video is helpful. But could you please redo the video, I couldn't see the full screen
nice and very informative. pl upload some more about instrument parameters
Great video! All these videos are very helpful and help me a lot. Thank you for uploading them!
thanks for the video it`s very useful..... what program you use for peptide sequence identification ?
Great and very useful, thanks so much
Hi, thanks for the video. I don't understand why you don't write m/z value for the SIM experiment. As I understand, it's necessary to write that parameter to carry out it fragmentation (MSn).
Thanx for posting videos like these. I think next video with running real sample on lcms\ms would more helpful
please explain how to set up constant neutral loss in the method
great video !! thanks a lot. please could you do another video explaining the measurement settings and what the values mean?
Thank you. this was very informative
PLEASE Explain about PRM
You're even saving my butt from so far away. Thank you, Melissa!
Thank you so much Mellissa for the great shearing. If you have time we hope you have time to make more videos shearing about setup LCMS and optimization to enhance peptide coverage (%) of Cytochrome C digestion.
It is a very nice video. Thank a lot. I recomend spanish subtitles for Latinamerica.
Hi. By using the image lab software, can you select and work with 2 or more bands per lane. For exemple if my antibody recognizes 3 isoforms of a protein and detects 3 bands. ? Thanks
a trick: watch movies on flixzone. I've been using them for watching loads of movies lately.
@Kellen Jaxtyn definitely, I've been using Flixzone} for years myself :D
where is your housekeeping gene? do we need it in quantification?
I was wondering about that too, you definitely need it for quantification.. i think what she means with "standard" is just the positive control sample
what should be the standard?
Great video! It has been a while since I worked on the instruments, watching this really helped jogging my memory.
Thanks a lot for posting, exactly what I was looking for :)
This is such a great video. Thank you for taking the time to put this together
Thansk again, it helps me a lot for my thesis. please upload more and more
Thanks so much for such a wonderful introduction, could please upload more about chromeleon and other software used in Q exactive Plus
Hi, we are about to buy a LC-MS system for biopharmaceuticals. How can I contact you to do some questions?
Great video...learnt a lot about lc!!!!!
Hello Melissa! Where do you add the column in the result section “found in sample”? Thanks for the video!
In the top left corner of the data table (right above the number 1, to the left of "checked") there is a button where you can add or delete more columns.
In the result output page, click the grid icon next to the proteins tab and you can select the different output tabs you want to view
Hi Mam Greetings!!! NICE VIDEO I am also working on Q Exactive in the analysis of Proteomics as well as API, Drug discovery molecules. if possible kindly make a presentation on what are the parameters effecting the method development in MS (LIKE tune page parameters).it is more helpful . i would like to request you please provide any data to know about method development parameters in orbitrap MSMS and my wats app no +91 9560627527 my mail id - grsnaidu1987@gmail.com valuable
Srry mam but the screen is not fully visible in the video
Thank you so much.