When discussing gene expression levels, it is important to consider whether it is the amount of mRNA or the amount of Protein. This is because mRNA and Protein levels do not necessarily correlate. It has not been clarified how many genes exist in each cell for which mRNA and Protein levels do not correlate, and whether these genes are important for the cell. In this study, we found that pluripotent stem cells such as iPS cells and ES cells have many such uncorrelated genes, and that these genes are essential for cell survival. There are still many mysteries regarding the regulatory mechanisms of Protein levels in different cell types, and we hope to unravel these mysteries in the future.

There are two points that I have found frustrating in my work with protein analysis using mass spectrometry. First, many researchers believe that there is no particular need to measure Protein levels because RNA can measure gene expression to some extent. Second, although it is well recognized that there are genes for which mRNA and Protein levels do not correlate, there are few findings that discuss the importance of these genes. I hope that this paper has created a stir on those points.
The most difficult point was to measure protein levels accurately, and we went through a lot of trial and error both experimentally and analytically. In the process, I was able to publish one quantitative analysis paper in 2019, and I was able to engage with a variety of researchers in making this article.
I was promoted to Junior Associate Professor & Independent PI on 4/1, the Revise deadline was 4/1, I submitted the paper in the evening, and when I went to Chion-in Temple to see cherry blossoms and came back, the paper was Accepted in principle. I was scared that it was April Fool.

Recently, labeling methods for comparative quantification, such as iTRAQ and TMT, are widely used, but there is a problem that the quantification accuracy is low. This low accuracy is caused by the usage of label peaks for quantification derived from multiple peptide ions. Although there are several solutions available, we proposed a method called RiMS (Removal of interference MS / MS spectra) and released a script written in Perl. The combination of Purity> 80% and RiMS suppresses the decrease in the number of identifications and improves the quantitative accuracy, so we are currently analyzing using the combined method.

This is a paper that Iwasaki wrote for the first time as a corresponding author. I also like the good numbers of 2019/01/30 on submit and 04/30 on accept. Responding to the reviewer's comments, the paper became better. I would like to thank the reviewers and improve myself to be able to comment like this. Also, two ph.D. students from our institute went out to eat well food together for the celebration of this paper. When they get a ph.D., I would like to celebrate at a pretty good place in Kyoto.

Protein sequences of prokaryote such as Escherichia coli contain a lot of cysteine. However, there is no enzymes to cleave cysteine ​​residues. Here, we improved the protein identification efficiency of Escherichia coli by optimizing the chemical digestion method of cysteine ​​residue.

This is the first paper of Dr. Iwasaki life. Supervised by Dr. Ishihama, I thought that it was quite hard to publish a scientific paper. I was astonished by the number of papers I had to read for writing the introduction. Then, the revice experiment (for me at that time) was pretty tough. I was living in the laboratory for almost a month during the cold winter in Tsuruoka city, Yamagata prefecture. At the end of the revise experiment, I was back to my house at bicycle around 3 AM. I pledged my heart to "I will not return in the middle of the night" because someone chased me by a car and I was so scared.