Proteome Discoverer Training Videos

Here are the current Proteome Discoverer 1.4 tutorial videos on Vimeo.  Please watch these in "HD", or they look terrible.  

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

10 comments:

  1. 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?

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  2. 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?

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

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  4. 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

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  5. 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 !!!

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    Replies
    1. 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.

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  6. 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

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    Replies
    1. 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.

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  7. 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?

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  8. 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

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