I don't have experience with the first part of your question, but I there is a lot of material available from the companies that sell the LC-MS machines (e.g. Thermo Fisher).

The easiest way to get primers for a region of DNA that codes for a peptide is to hope that your organism has a well-annotated sequenced genome. Use NCBI BLAST to get the genome sequence & the built-in primer designing tools. I hope that helps!

Hi Bhargavi,

You need to subject the .raw file to a protein database search engine. Mascot, MaxQuant, Proteome Discoverer, Protein Prospector, Sequest are all search engines which accept the .raw file as a .raw file or extracted peak files from the .raw file.

MSConvert is a tool that can take a .raw file and create "mgf" file which is a format that eg., Mascot search engine accepts for database searching.

You will also need a .fasta file, from UniprotKB site

https://www.uniprot.org/help/uniprotkb

which contains protein sequences, usually of your source of protein, eg., human, rodent etc. Some search engines are freely downloadable, for others, you will need a license or free trial license.

Once you identify your protein, you can inspect the amino acid sequence. Katie's answer above can direct you to the right place to be able to design your primers.

I hope this helps, good luck!

Hediye.

Thank you so much mam. This is definitely going to help me a lot. I have given my samples for MS/MS, once I get the raw data I will proceed as mentioned above.

Thank you for your time.