Q&As About Proteomics (Q11-Q15)

Q11. In which journals are proteomics experiment related articles ususlly published? What are the differences?

MCP (Molecular & Cellular Proteomics): impact factor 7
JPR (journal of proteome research): impact factor 5
Proteomics: impact factor 5
Journal of Prteomics: impact factor 5
Electrophoresis: impact factor 5
Plos One: impact factor 5
Other magazines: BMC Genomics, Expert Rev Proteomics, BMC Syst Biol, OMICS, Proteomics Clin Appl, Proteome Sci, etc.

Q12. What techniques need to be repeated? Which one is used in the repeated experiment, biological repetition or technical repetition?

Label free needs to be repeated for three times, so do iTRAQ and TMT. If a large number of verification experiments such as WB or ELISA are designed in the experiment, it is better to repeat them twice. If the experiment is not repeated and there are only a few verification experiments designed, the publication of the article may be affected as the reviewers may question your results, magzines with impact factor in particular. they are determined to publish high. Therefore, researchers who are determined to publish high-level articles are recommended to design experiment repeation in their experiments. If technical repetition is performed, the data repeatability between the results of each experiment will be better, and biological repetition may lead to repeatability bias for various reasons. In general, for label free, it is better to use technical repetition, which is beneficial to subsequent data analysis. While, other experiments can use either biological repetition or technical repetition. For metabolome, select appropriate amount for biological repetition according to different samples.

Q13. How to determine which proteins are related to their own research, and what kind of proteins to select for verification experiments later?

Researchers need to use relevant biological background of their research, combine it with the results of bioinformatics analysis, and review the relevant literature to confirm which proteins can be used for further in-depth research.

Q14. In sample delivery, which sample requires low temperature? Which requires room temperature? And dry ice?

Samples such as cells, tissues, protein solutions, and bacteria are prefer to be transported with dry ice. SDS-PAGE strips, 2D spots and the enzymatically hydrolyzed peptide samples can be directly transported at room temperature. In other words, samples that require protein extraction or good protein extraction (easily degradable) require low-temperature transportation, while proteins in gel or peptides that are enzymatically hydrolyzed can be transported at room temperature.

Q15. Which samples need high abundance protein removal? How to remove?

In general, high-abundance proteins (albumin and other immune proteins) are present in serum and plasma samples. If the client provides such samples, it is necessary to communicate with he/she in advance that it is necessary to remove the high-abundance protein. Currently, there are mature reagents that can remove high abundance proteins from the serum.

Samples such as body fluids and cell culture fluids also contain high-abundance proteins. If high-abundance proteins are present in such samples, it is necessary to first identify the common immune proteins by mass spectrometry, and then use high-abundance protein removal kits to remove them.

The presence of high abundance proteins in other samples is not common. If they are found during the experiment, refer to the solution above. Other samples may exist high-abundance proteins that cannot be removed with a suitable kit. In this case, the customer must be informed with the risk in advance.

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