Proteome Discoverer Videos


This is the complete list of videos for Thermo Scientific's Proteome Discoverer version compiled by me and some others over the years.  As always, please watch all videos in HD for best resolution. Sorry about the sound and my squeaky voice.

 PROTEOME DISCOVERER 1.4

New in PD 1.4:  https://vimeo.com/64512755
FASTA databases:  https://vimeo.com/62262575
Configuring Mascot:  https://vimeo.com/64511819
Getting started with the PD 1.4 Daemon:  https://vimeo.com/64546865
Setting up/using spectral libraries:  https://vimeo.com/62355749
Setting up a simple workflow:  https://vimeo.com/64502054
False discovery (PSM validation) nodes:  https://vimeo.com/64465036
Workflow templates (exporting/importing):  https://vimeo.com/63694431
Using the annotator node:  https://vimeo.com/63687734
Running an iTRAQ/TMT experiment:  https://vimeo.com/64518114
Processing SILAC data:  https://vimeo.com/62260286
Label free quan experiments (PIAD):  https://vimeo.com/62280924
Processing neutral loss triggered MS2 LTQ data:  https://vimeo.com/63691742
Processing neutral loss triggered MS2 Q Exactive data:  https://vimeo.com/63696432
Exporting unmatched spectra for de novo or PTM analysis:  https://vimeo.com/63693490
Installing MSAmanda:  https://vimeo.com/64503144
Multi-enzyme processing in PD 1.4:  https://vimeo.com/64506696

PROTEOME DISCOVERER 2.0/2.1


1.       Loading a FASTA database from your hard drive: https://vimeo.com/115595009
2.       Creating a custom FASTA database:  https://vimeo.com/115594400
3.       How to use the Administration menu:  https://vimeo.com/117010043
4.       How to configure your Mascot server:  https://vimeo.com/117042117
5.       How to set up a simple peptide ID workflow in PD 2.0:  https://vimeo.com/115592929
6.       How to use the consensus steps in PD 2.0:  https://vimeo.com/115593122
7.       How to process M2 TMT and iTRAQ MS2 data:  https://vimeo.com/117051567
8.       How to organized a reporter quan experiment in PD 2.0 (Part I): https://vimeo.com/121393236
10.   How to organize a reporter quan experiment in PD 2.0 (Part 2, the results): https://vimeo.com/121394251
11.   How to process SILAC data:  https://vimeo.com/115874330
12.   Reprocess consensus report data in PD 2.0 (new version) :  https://vimeo.com/121897580
13.   How to perform label free relative protein quan in Proteome Discoverer 2.0: https://vimeo.com/117064754
14.   How to set up a complex relative label free quan experiment in PD 2.0 (multiple fractions):  https://vimeo.com/121074081
15.   How to use the Annotation nodes:  https://vimeo.com/121397080
16.   How to use the Proteome Discoverer 2.0 Daemon:  https://vimeo.com/115875441
17.   Set up a search with multiple search engines:  https://vimeo.com/115594605
18.   How to export data to search in another program:  https://vimeo.com/63693490
19.   Peptide FDR discussion (PSM validation nodes): https://vimeo.com/64465036

20.   Protein Validation nodes:  https://vimeo.com/121399307

21.  How to extract only proteins with a specific post-translational modification: https://vimeo.com/131230075
22.  How to process global peptide and global prosphoproteomics data together into one single report: https://vimeo.com/137643323

PROTEOME DISCOVERER 2.2

 Setting up Proteome Discoverer 2.2 for first use: https://vimeo.com/216704831/dcdd4b7384
Adding FASTA files from Hard Drive (from my PD 2.0 videos): https://vimeo.com/115595009
How to configure your Mascot Server (from my PD 2.0 videos): https://vimeo.com/117042117
What is the SpectrumRC node and how do you use it?  https://vimeo.com/216737928/bfc09afe5f
Getting started with label free quan with Minora!  https://vimeo.com/216690621/95caaff85c
A more in-depth look at the precursor ion quantification nodes:  https://vimeo.com/216734570/3b3546c44b
Looking at the Minora results: https://vimeo.com/216699979/fe1ed3bb4c
Finding what is significantly different in your data with Volcano plots: (Updated Link)
Reporter ion quantification report output:  https://vimeo.com/216702197/292d44c572
Using Filters and setting default filters for PD 2.2:  https://vimeo.com/216718011/d4e05cbf40
Optimizing the MSF Files consensus node: https://vimeo.com/216722376/204a582cf0



16 comments:

  1. SantoshMarch 14, 2014 at 3:31 AM

    I have question regarding Label free quan experiments (PIAD): https://vimeo.com/62280924. You have selected precurssor ion detector in the quantification experiment. However there is one more option which precursor ion quantifier. Can you please share your thoughts on this?

    ReplyDelete
  2. BenMarch 14, 2014 at 12:55 PM

    Santosh,
    There are two quan settings with surprisingly similar names. The "area" detector is for label free quan. The other one is the SILAC type experiment. Does this clarify?

    ReplyDelete
  3. SantoshMarch 16, 2014 at 3:09 AM

    Ben. Yes clear now. Thanks for the prompt reply..

    ReplyDelete
  4. SantoshMarch 16, 2014 at 3:16 AM

    Hey Ben, Few more questions on label free quan using PD 1.4. If i have lets say 4 technical replicates of my sample, so after uploading the raw files in a workflow template. Whether the PD will merge my tech replicate and will give combined result of that particular sample? and the other question is, is it possible to do LFQ of several case control pairs with replicates at a time on PD 1.4

    ReplyDelete
  5. Mark WingerdApril 9, 2014 at 11:21 AM

    Hi Ben,

    Do you have anything on setting up a very basic Workflow for
    an Orbitrap XL using only CID, with 1 hi-res Orbitrap scan
    followed by 8 linear trap MS/MS scans ????

    And all of the recommended parameters ?

    Thanks,

    Mark

    BTW: Great Job on thee.
    Best PD Resource out there, bar NONE !!!

    ReplyDelete
    Replies
    1. BenApril 15, 2014 at 7:32 AM

      Mark,
      Thanks! I'm glad you find this useful. I should have exactly that method floating around here somewhere from my postdoc. Can you send me a request to orsburn@vt.edu so I have a reminder and your email address? I'll try and get it to you in the next day or so.

      Delete
  6. UnknownAugust 28, 2014 at 9:36 AM

    Hi Ben,

    I am wondering how I can do labeling methods if i have PD 1.3 and not 1.4. What can i do or use in such case? Thanks for your help

    ReplyDelete
    Replies
    1. BenAugust 30, 2014 at 10:05 AM

      Hi,
      Absolutely! If you have the quan version of PD, everything from 1.1 (I think...defnitely 1.2) can do labeled quantification.
      But, unless there is a definite reason you have to stay on PD 1.3, the upgrade to PD 1.4, in most cases, is free. And it is substantially better.

      Delete
  7. Leandro X. NevesJanuary 25, 2015 at 12:49 PM

    Hi Ben,

    I have used "area detector" node to perform label-free quantification on PD 1.4. I noticed that protein areas may change depending on the manner I deal with my data. Working with triplicates I can select the three .raw files and perform only one search, however, it is possible to search them separately and open a unique report sheet merging the three independent runs. I am wondering what's the best way to do that, could you give an advice?

    ReplyDelete
  8. JazmínNovember 10, 2016 at 8:43 AM

    Hi Ben,
    Thank you for put together all these tools are very useful. I am quite new at iTRAQ proteomics and I'm using PD1.4. I have been struggling fpr a while dealing with missing quan values. I am comparing a control group (3 tags) and a diseased one (4 tags) (one tag for a master pool), and we are very interested in the proteins that are exclusively expressed for the diseased group, but the ratios of these proteins are not reported as you can suppose. Could you recommend a strategy to find this specific group of proteins? Any help is greatly appreciated.
    Diana

    ReplyDelete
  9. UnknownMarch 7, 2018 at 10:52 AM

    This is amazing. Thank you

    ReplyDelete
  10. Joe OttoMarch 28, 2018 at 6:40 AM

    Hey Ben,
    It looks like the PD 2.2 video links are not working. Just letting you know and hope you can get them back up soon. I'm looking into PD 2.2 LFQ stuff and was just about to watch those videos :)

    ReplyDelete
  11. UnknownSeptember 5, 2018 at 2:43 AM

    Hi Ben,

    thank you for the dissemination of information in the field of proteomics.
    I watched your videos regarding the use of different versions of proteome discoverer related to SILAC (1.4 and 2.0).
    I have version 2.2 and some noode that you have in other versions of proteome discoverer are not exactly the same in 2.2. Do you have any advices to build a SILAC WORFLOW: labeled versus unlabeled and the relevant parameters to use ?

    ReplyDelete
  12. AnisFebruary 1, 2019 at 10:00 AM

    Regarding glycopeptides what is the best workflow please?

    ReplyDelete
  13. UnknownApril 22, 2019 at 11:27 AM

    Hi

    I am not able to see the fasta files in Mascot search. How can get those in if I select the Mascot search option?

    Thanks for the help

    ReplyDelete
  14. Zardoz53March 29, 2020 at 11:10 PM

    This link to this video is not working- Finding what is significantly different in your data with Volcano plots: (Updated Link)

    ReplyDelete

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