RNA-seq advantage over Proteomics approach

[bioman1]

What are the advantages of RNA-seq experiment over proteomics approach in identifying secreted protein?.

[mbblack]

What are the advantages of RNA-seq experiment over proteomics approach in identifying secreted protein?.

In what context? RNA-seq detects the RNA products of expressed genes. Proteomics actually detects peptides. The two technologies are very different, and intended for the detection and measurement of very different molecules.

Also, RNA-seq may tell you a gene is being expressed, but it does not necessarily tell you any thing about actual protein levels in living cells. Similarly, a proteomics experiment may tell you about the presence and abundance of a particular functional protein, but does not necessarily tell you a thing about gene expression.

[Cytosine]

I believe using proteomics approaches to indentify secreted proteins is the way to go.

As mbblack said, RNA-Seq will not tell you enough about the protein level in the sample and will give you another layer of work for having to translate the transcripts into final protein products.

[bioman1]

Thanks for the comments.

@mbblack: I some article finding secreted protein through RNA-seq by using bioinformatics tools like signalp, TargetP, secretome etc they identify secreted protein.

1. Is RNA-seq is cheaper than proteomics approach to identify secreted proteins?
2. Is RNA-seq is advantage if it is non-model plant?

[mbblack]

Thanks for the comments.

@mbblack: I some article finding secreted protein through RNA-seq by using bioinformatics tools like signalp, TargetP, secretome etc they identify secreted protein.

1. Is RNA-seq is cheaper than proteomics approach to identify secreted proteins?
2. Is RNA-seq is advantage if it is non-model plant?

SingalP (and other such tools) predict the presence of signal peptide cleavage sites in gene sequence data. That is not at all the same thing as actually detecting, identifying and showing the presence of a protein.

RNA-seq is literally incapable of identifying a secreted protein. RNA-seq data can make predictions about proteins and functional sites based on sequence data, in that it can detect the presence of genomic transcripts coding for a protein. Proteomics actually detects and measures proteins themselves. For most questions, one cannot take the place of the other.

So if you need to confirm the presence of a specific protein and measure its abundance, or you need to identify a number of related proteins and measure their relative abundance, then RNA-seq cannot do that for you.

So again, what exactly is your experiment intended to do, or what exactly is it you need to measure and identify? Is it actual protein(s), or do you want gene expression information about the genes coding for specific peptides or proteins?

P.S. especially if you are working on a non-model organism or species, and you actually need to demonstrate the presence of a specific protein, then you need proteomics data. Nobody is going to accept predicted presence from gene expression data as hard evidence of the actual presence of a specific protein or metabolite.