Dear Richelle,

I am forwarding you the mail id of my senior, Adeel. He is well aware of analyzing these types of data. You can get in touch with him at [email protected]  .... He will definitely be of great help to you...

Best of luck

Hi, 

Few preliminary questions

- What mass spec did you use?

- what proteomic software did you use?

The general workflow is divided in two steps:

Identification

You can claim protein identification when you have at least TWO unique peptide.

A unique peptide is a peptide with a sequence which belongs to ONLY 1 isoform of a protein.

If this is not the case, you can claim identification of a protein family (if the sequence is shared by different isoforms).

If a peptide is belonging to different proteins (completely different families) then you cannot assign it.

Quantification

In the case of unique peptides, you need to average the ratio of each peptide (which will give you a value with an SD). This is what you use to calculate the final protein ratio between two samples.

Significance

There is not a REAL rule. There are proteins that produce a biological effect if their expression increases by a factor 1.5, other needs a factor 3 etc...

The best you can do is:

- List all of the ratios

- Highlight ratios >2  and