The jPOST repository has been managed since 2016. Here, we summarize the contents of the registered projects and the newly developed functions implemented in the repository.

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Neurofibromatosis type 1 (NF1) tumor suppressor gene product, neurofibromin, has a function as a Ras-GAP, a negative regulator of Ras. The loss of neurofibromin is known to cause aberrant differentiation and proliferation of neural cells in NF1 patients with unknown mechanisms. To clarify the molecular mechanism of NF1 pathogenesis, we prepared a NF1 disease model using NF1 gene knockdown (KD) in PC12 cells [1,2,3], and analysed their mRNA and protein expression profiles with a unique integrated proteomics approach, comprising iTRAQ, 2D-DIGE, and DNA microarrays, using an integrated protein and gene expression analysis chart (iPEACH) [1,4]. In this study, time course quantitative proteomics of NF1-KD PC12 cells after nerve growth factor (NGF) treatments comparing with control wild cells were performed by iTRAQ quantification. The data described in this paper have been deposited to jPOST [5,6] with the identifiers JPST000067.

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Protein phosphorylation is the major molecular mechanisms in the regulation of cellular functions and dynamically coordinate their signaling networks. Aberrant regulation of protein phosphorylation has been linked to a wide variety of human diseases, including cancer, immune abnormalities, and diabetes. With recent advances in liquid chromatography coupled to tandem mass spectrometry (LC-MS), phosphoproteome analysis has become a major area in biomedical research. Several chemoaffinity-based methods for enrichment of phosphopeptides have been developed, and in these methods, nucleic acids in the cells interfere with the binding of the phosphopeptides to affinity beads, thereby reducing the efficiency of enrichment. Here, we introduce a chemoaffinity-based method for enrichment of phosphopeptides in combination with protein extracts excluded of nucleic acids to improve the efficient enrichment of phosphopeptides.

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For the analysis of mass spectrometry data from proteome samples, several steps must be paid attention to, the first of which is the generation of peak list. Although programs distributed by mass spectrometer vendors, or mscovert.exe by ProteoWizard [1] are commonly used to generate peak lists; these may not be suitable for the purpose. Herein, we have implemented single function tools to solve these problems. For example, raw data files generated by modern high-performance mass spectrometers may result in huge .mgf files of more than 500 MB, which are time-consuming to perform database search and may cause communication errors to the computational server; e.g. the Mascot server. Our PeaklistSplit splits the files to reduce the search time per search. As the precursor ion for each product ion spectrum, the mass spectrometer tends to select the peak with the greatest intensity in the isotope cluster of interest, not necessarily the monoisotopic ion, and the m/z of the precursor ion may not be properly recorded, especially in the case of high molecular weight ions. We have thus created two tools to address this issue: ProteoWizardPlist and ProteoWizardPlistW. In addition, for use in the ongoing proteome database jPOST [2,3], multiple peak lists are generated from a single raw data in some cases. We developed PeakListMerge, a tool to merge multiple peak lists into a single list to control the false discovery rate based on target-decoy search [4,5].

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The Japan Computational Mass Spectrometry (JCompMS) group was launched in 2016 as a special interest group of the Japanese Society for Bioinformatics (JSBi). It aims to facilitate research communications, protocol exchanges, and further developments of computational mass spectrometry (compMS) in Japan. JCompMS aims to organize data science projects in multi-omics utilizing mass spectrometry such as proteomics, glycomics, lipidomics and metabolomics; currently, its main activities include organizing symposia, workshops, lectures, and hackathons related to compMS research. In this report, we introduce the activities held in 2020 and review the current informatics research on omics using mass spectrometry data in Japan.

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