Help for proteomics!!!
radha arumugam
Tuesday, 28 April 2009 12:39 UTC
Dear All,
I am new to this and happy to introduce myself as Ms Radha from India , pursuing doctoral degree in the field of proteomics. My work mainly encompasses on the determination of homogeneity of secretory proteins of mullerian galnad of caecilian ( an amphibian) with that of the mammalian accessory reproductive glands. By far, I have isolated the secretory proteins from all the glands and found the homogeneity of proteins with respect ot molecular weight. Further I intend to do, the 2D page and Maldi. But, my doubt is that, the genome sequence for the none of the secretory proteins of the mullerian gland is available now. So, will it be possible to do the Peptide mass fingerprinting for my proteins??Kindly reply. Thank you in advance
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Replies
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Dear Radha,
I hope this is possible and that is the beauty of technique, once you get the mass of your protein than you can search in data base for the homologous sequences that of your protein peptide mass. Since it mammalian protein so lot of data base is present on internet, although there is slight variabilty in term of species but it s not very significant. So go ahead and come up with some novel sequences -
Dear Radha,
i’m working in identification of proteins from non-sequenced organisms by mass spectrometry. I hardly think that you can obtain trusting results by MALDI TOF MS and Peptide mass fingerprint. This technique is based on the mathematical correspondence beetwen your measured peptide masses and the theoretical masses obtained by in silico digestion of the proteins in the databases. The only chance to have a significant result is that you have digested a protein with, at least, around 60-70% of identical peptides.In my experience this is almost impossible, unless you are working with very relate organisms like mammalian are.
I reccomend you to use a technique able to give you MS/MS information (Q-TOF, TOF-TOF) in order to try some homology search. Recently, I have worked with proteins from mussel (Mytilus galloprovincialis), the results was so disappointing also using de novo sequencing.
I hope you find that information regarding useful!
Good luck!
Francesco -
Dear Francesco Marsano,
Thank you for your kind reply. Of course, I am doing homology search only. I have done MALDI, but the results are not quite satisfactory. Anyway I will try with Q-TOF. -
Anonymous
Hi all!
My name is Stella and I am a PhD student in Germany, working in a proteomics department. I got one question that I could not solve alone til now and I am wondering if anyone from you can help me. I must analyse nucleus extracts from liver tissues but in our Institute the only SOP that explained that forbids to use tissues already frozen. Do anyone from you know an alternative protocol for that? (My samples are at -80C)!
I thank you all in advance,
sincerely,
Stella
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