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A draft map of the human proteome.

Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A - Nature (2014)

Bottom Line: However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet.In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans.A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames.

View Article: PubMed Central - PubMed

Affiliation: 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

ABSTRACT
The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

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Identification of novel genes/ORFs and translated non-coding RNAsa, An example of a novel ORF in an alternate reading frame located in the 3’ UTR of CHTF8 gene. The relative abundance of peptides from the CHTF8 protein and the protein encoded by the novel ORF is shown (bottom). b, An example of translated non-coding RNA identified by searching 3-frame translated transcript database. The MS/MS spectrum of one of the five identified peptides (LEVASSPPVSEAVPR) is shown along with a similar fragmentation pattern observed from the corresponding synthetic peptide.
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Figure 9: Identification of novel genes/ORFs and translated non-coding RNAsa, An example of a novel ORF in an alternate reading frame located in the 3’ UTR of CHTF8 gene. The relative abundance of peptides from the CHTF8 protein and the protein encoded by the novel ORF is shown (bottom). b, An example of translated non-coding RNA identified by searching 3-frame translated transcript database. The MS/MS spectrum of one of the five identified peptides (LEVASSPPVSEAVPR) is shown along with a similar fragmentation pattern observed from the corresponding synthetic peptide.

Mentions: We identified eight cases where we observed peptides that mapped to an ORF located in an alternate reading frame within coding regions of annotated genes. For example, we identified peptides that mapped to a novel ORF of 159 amino acids within the C11orf48 gene. The protein encoded by the C11orf48 gene was identified only in the adult retina although we identified three peptides encoded by the novel ORF from 17 various cells/tissues. We also identified peptide matches to seven ORFs located within 3’UTRs. As an example, a novel ORF comprising of 524 amino acids in the 3’UTR of the CHTF8 gene was identified on the basis of multiple peptides. The translation initiation site of this novel ORF overlaps the stop codon of the CHTF8 gene (Extended Data Fig. 4a). Remarkably, the protein encoded by this novel ORF was observed in hematopoietic cells where we did not detect the CHTF8 protein. In addition, this novel gene product was expressed at higher levels in fetal ovary and adult testis than the protein encoded by CHTF8. These observations suggest that the translational control for these two proteins encoded by the same gene structure is likely different. We also identified a peptide encoded by an ORF within a human endogenous retrovirus (Extended Data Fig. 5b). Domain analysis revealed the presence of a signal peptide at the N-terminus along with other domains including Furin-like repeats. In fact, during preparation of this manuscript, a report was published in which this protein was designated as suppressyn and shown to inhibit cell-cell fusion in trophoblast cells28.


A draft map of the human proteome.

Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A - Nature (2014)

Identification of novel genes/ORFs and translated non-coding RNAsa, An example of a novel ORF in an alternate reading frame located in the 3’ UTR of CHTF8 gene. The relative abundance of peptides from the CHTF8 protein and the protein encoded by the novel ORF is shown (bottom). b, An example of translated non-coding RNA identified by searching 3-frame translated transcript database. The MS/MS spectrum of one of the five identified peptides (LEVASSPPVSEAVPR) is shown along with a similar fragmentation pattern observed from the corresponding synthetic peptide.
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Figure 9: Identification of novel genes/ORFs and translated non-coding RNAsa, An example of a novel ORF in an alternate reading frame located in the 3’ UTR of CHTF8 gene. The relative abundance of peptides from the CHTF8 protein and the protein encoded by the novel ORF is shown (bottom). b, An example of translated non-coding RNA identified by searching 3-frame translated transcript database. The MS/MS spectrum of one of the five identified peptides (LEVASSPPVSEAVPR) is shown along with a similar fragmentation pattern observed from the corresponding synthetic peptide.
Mentions: We identified eight cases where we observed peptides that mapped to an ORF located in an alternate reading frame within coding regions of annotated genes. For example, we identified peptides that mapped to a novel ORF of 159 amino acids within the C11orf48 gene. The protein encoded by the C11orf48 gene was identified only in the adult retina although we identified three peptides encoded by the novel ORF from 17 various cells/tissues. We also identified peptide matches to seven ORFs located within 3’UTRs. As an example, a novel ORF comprising of 524 amino acids in the 3’UTR of the CHTF8 gene was identified on the basis of multiple peptides. The translation initiation site of this novel ORF overlaps the stop codon of the CHTF8 gene (Extended Data Fig. 4a). Remarkably, the protein encoded by this novel ORF was observed in hematopoietic cells where we did not detect the CHTF8 protein. In addition, this novel gene product was expressed at higher levels in fetal ovary and adult testis than the protein encoded by CHTF8. These observations suggest that the translational control for these two proteins encoded by the same gene structure is likely different. We also identified a peptide encoded by an ORF within a human endogenous retrovirus (Extended Data Fig. 5b). Domain analysis revealed the presence of a signal peptide at the N-terminus along with other domains including Furin-like repeats. In fact, during preparation of this manuscript, a report was published in which this protein was designated as suppressyn and shown to inhibit cell-cell fusion in trophoblast cells28.

Bottom Line: However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet.In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans.A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames.

View Article: PubMed Central - PubMed

Affiliation: 1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

ABSTRACT
The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here we present a draft map of the human proteome using high-resolution Fourier-transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples, including 17 adult tissues, 7 fetal tissues and 6 purified primary haematopoietic cells, resulted in identification of proteins encoded by 17,294 genes accounting for approximately 84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading frames. This large human proteome catalogue (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

Show MeSH
Related in: MedlinePlus