The Systematic Platform for Identifying Mutated Proteins (SysPIMP)
Introduction
The Systematic Platform for Identifying Mutated Proteins (SysPIMP) was designed and developed for identifying human disease-related mutated proteins from mass-spectrometry (MS). For achieving this goal, we collected human mutated sequences known to be related to diseases till now. After surveying mutated sequence sources: PMD, OMIM, SwissProt polymorphism, HGMD and etc, we found that currently HGMD contains the largest human gene mutation information. However, for academic users HGMD does not provide with whole data download service, finally we decided to systematically extract and curate mutation information from PMD, OMIM, SwissProt, MSIPI database to form SysPIMP and let it free for academic users.
In OMIM database, Allelic Variants (AV) field describes disease-related mutated sequences in each OMIM term through the literature survey with experts' curation. If users want to get the original mutated protein sequence from AV field, further efforts should be paid for reading through attached literatures, doing Blast searches, and etc. Even then, contradictory statements will emerge quite often. For reducing misleading information and recovering mutated sequences based on mutation information, we developed the pipeline which recovers amino acid sequence based on gene name from OMIM and collective human normal proteins, called as Integrated annotated Human normal Proteins (IHP). For generating IHPs, seven different sources: four versions of human genomes (Ensembl 48, Celera, HuRef and Ref assemblies in NCBI; See also Human Genomes under Integrated Mutated Sequence), Swissprot sequences, normal sequences deposited in PMD and MSIPI (See IHP statistics). Based on IHPs, 19,948 sequences were recovered (See OMIM Mutated Sequence Browser). Taken together with other mutated sequences, 34,891 non-redundant human mutated sequences related to diseases were obtained (See Integrated Mutated Sequence Browser and Statistics page).
Based on archived IMSs, integrated X!Tandem, one of MS results analysis tools, will provide identification of human disease-related mutated sequences from mass-spectrometry (MS) results. Four different interfaces for presenting X!Tandem result were displayed in X!Tandem History Browser.
