Converting peak ID to gene symbol

Question

[zizigolu]

Hi I have a list pf peak IDs from a proteomics experiment like

How I can convert peak ID to gene symbol (human)

[GenoMax]

There is no information here that can be used to help you. Those ID's are not in any standard format and could mean anything. Add more info/context if you can.

[Alex Reynolds]

It would be helpful to describe your data in more detail. Knowing what format of data you're using may help with recommending the right conversion and querying tools.

[zizigolu]

Thank you, you are right

In this paper https://www.sciencedirect.com/science/article/pii/S1874391913000444?via%3Dihub supplementary file https://ars.els-cdn.com/content/image/1-s2.0-S1874391913000444-mmc4.xlsx lists differentialy expressed proteins between different tissues but in terms of mass spectra (peak m/z). I want to convert these peak IDs to gene symbol to get commonality from my data but whatever I googled I did not find a clue

Answer 1

[Alex Reynolds]

The paper suggests a tool called "ClinProt Tools" may have been used for peak calling, but what I could find online about this tool doesn't include much detail about the format they use for peak IDs. I would suggest getting in touch with the paper's authors and ask them for more comprehensive details about the peak IDs and where they come from — this will probably get you to the fastest and most correct answer.

[Alex Reynolds]

I should warn that proteomics is not my field, but the format of those peak IDs gets no hits on either of the two search engines I use, so contacting the authors will probably be the best way to get an answer. Good luck!

[zizigolu]

The response from corresponding author

 The approach we used (MALDI profiling) is a high-throughput mass spec method that measures the abundance of multiple proteins and generates a fingerprint/profile that potentially enables discrimination between samples e.g. cancer versus adjacent normal.  One of the disadvantages of this method is that it measures the abundance of multiple protein entities but does not provide any identification of the proteins underlying the profile.   A lot of additional experimental work is necessary to identify the proteins underlying the peaks in the profiles – so unfortunately it will not be possible to quantify your proteins of interest from our data.

    ClinProt Tools is a software from Bruker for analysing/comparing the profiles (not protein identification).

[Alex Reynolds]

Thanks for following up — this may help other people who have similar questions down the road.