Beginner: How to prepare MS data to import to Cytoscape

[Ivy Ngai]

I got some protein MS searching result files from MaxQuant (in excel format), and I am tying to do a network analysis with Cytoscape, but I failed to find any online tutorial about how to transfer the MS results to the format that can be import to Cytoscape

[Scooter Morris]

Hi Ivy,
    You can read your excel format into Cytoscape directly.  Just choose the appropriate column to use for your key identifier.  Since you are using MaxQuant, I assume you just have a list of proteins, so you aren't really going to have a network after your import.  What kind of network analysis are you trying to perform?

-- scooter

On 02/12/2016 04:22 AM, Ivy Ngai wrote:

I got some protein MS searching result files from MaxQuant (in excel format), and I am tying to do a network analysis with Cytoscape, but I failed to find any online tutorial about how to transfer the MS results to the format that can be import to Cytoscape

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[Ivy Ngai]

Hey Scooter,

Many thanks for your reply, the net work I am try to do is a protein- protein interaction network, if I choose inport network from file then I think part from gene name column, I till need  a column for attribute, but I am not sure where to get this column. I also tried the inport network from web detabase, input all all the protein IDs, and merge the network, but not sure if it is the right way.

Also, afterwards I plan to combine my protein data with proteins of a ATCC strain bacteria, can I get the protein data of ATCC bateria from any database?

Thank you so much for your kind help!

Ivy

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[Scooter Morris]

Hi Ivy,
    I'm a little confused.   Where are you getting your PPI network?  Is it the result of an AP-MS data set?  If not, what are the identifiers (the node name column) used for the PPI network you obtained?  Once you know what the identifiers for your PPI network, then you need to find the matching identifier in your MS data set.

-- scooter

[Ivy Ngai]

Hi Scooter,

Sorry for the confused information, I am really new to this area. My protein sample is from a particular hunan tissue, and we are trying to do a protein−protein interaction network analysis, emphasizing its functional clusters like the attached paper.

[Scooter Morris]

Hi Ivy,
    OK, so in that paper, they took the list of proteins that had different levels between the groups and loaded it into IntAct to create a PPI network.  So, one way to create the initial network is to take your list of genes and paste them into the StringApp or GeneMania and create a PPI network.  Then you can use that network to import your MS data to get the actual values.  Not sure what you want to do from there, it really depends on what kind of conclusions you're working for.  You might perform some kind of cluster analysis with clusterMaker2 or overrepresentation analysis using ClueGo or BINGO.

-- scooter

[Ivy Ngai]

Dear Scooter,

Many thanks for your reply and explainations, They are quite helpful!

Actually We are trying to find functional connections between our protein sample and some bacteria strains, hence do you have any suggestions regarding PPI netwok between our human proteins and ATCC strain bacterial proteins, like where to get the protein database of ATCC strain, and how to import it together with my protein samples?

Thank you so much!

Ivy