Dataset Information

Identification of missing proteins in the proteome atlas of multiple healthy human tissues

ABSTRACT: We re-analyzed the deep proteome atlas of 29 paired healthy human from the published paper (Wang, Dongxue, et al. Molecular systems biology 15.2 (2019)) to identify missing proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart, Testis, Spleen, Urine, Brain, Embryo, Cotyledon, Blood Plasma, Liver, Cerebrospinal Fluid, Lung, Lymph Node, Kidney, Erythrocyte, Primary Cell, Placenta, Dendritic Cell, Endosperm, Rosette, Colon, Bone Marrow, Saliva

SUBMITTER: Sun jinshuai

LAB HEAD: Shujia Wu

PROVIDER: PXD021391 | Pride | 2020-11-17

REPOSITORIES: Pride

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Publications

Open-pFind Verified Four Missing Proteins from Multi-Tissues.

Wu Shujia S Sun Jinshuai J Wang Xi X Xu Feng F Chi Hao H Li Yanchang Y Zhong Bowen B Xie Yuping Y Yan Zhonghua Z Chang Lei L Wang Dongxue D He Fuchu F Wu Junzhu J Zhang Yao Y Xu Ping P

Journal of proteome research 20201110 12

The Chromosome-Centric Human Proteome Project (C-HPP) was launched in 2012 to perfect the annotation of human protein existence by identifying stronger evidence of the expression of missing proteins (MPs) at the protein level. After an 8 year effort all over the world, the number of MPs in the neXtProt database significantly decreased from 5511 (2012-02-24) to 1899 (2020-01-17). It is now more difficult to provide confident evidence of the remaining MPs because of their specific characteristics, ...[more]

PMID: 33172275

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Project description:In recent years, high-throughput technologies have contributed to development a more precise picture of the human proteome. However, 2,129 proteins remain listed as missing proteins (MPs) in the newest neXtProt release (2019-02). The main reasons for MPs are a low abundance, low-molecular-weight (LMW), unexpected modifications, membrane characteristics, etc. Moreover, more than 50% of the MS/MS data have not been successfully identified in shotgun proteomics. Open-pFind, an efficient open search engine, recently released by the pFind group in China, presents an opportunity to identify these buried MPs in complex samples. Proteins and potential MPs were identified using Open-pFind and three other search engines to compare their performance and efficiency with three large-scale datasets digested by different enzymes. Our results demonstrated that Open-pFind identified 29.9-47.5% more peptide-spectrum matches (PSMs), 48.0-63.9% more peptides sequences (with modifications) and 22.7-38.1% more peptide sequences (regardless of modifications) than those identified by the second-best search engine. As a result, Open-pFind detected 7.5-19.3% more candidate MPs than those by the second-best search engine. In total, 5 (PE2) of the 150 candidate MPs identified by Open-pFind were verified from two unique peptides containing more than 9 amino acids (AA) by using spectrum theoretical prediction with pDeep, and synthesized peptide matching with pBuild, after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant (SAAV) filtering. These five verified MPs can be ranked in the PE1 level. In addition, three other candidate MPs were verified with two unique peptides (one peptide containing more than 9 AA) and the other containing only 8 AA), which were slightly lower than the criteria listed by C-HPP, and required additional verification information. More importantly, unexpected modifications were detected in these MPs. Another 141 MPs were listed as candidates, but required additional verification information.

Dataset Information

Identification of missing proteins in the proteome atlas of multiple healthy human tissues

Publications

Open-pFind Verified Four Missing Proteins from Multi-Tissues.

Similar Datasets

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