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Hwang, Heeyoun,Park, Gun Wook,Park, Ji Yeong,Lee, Hyun Kyoung,Lee, Ju Yeon,Jeong, Ji Eun,Park, Sung-Kyu Robin,Yates, John R.,Kwon, Kyung-Hoon,Park, Young Mok,Lee, Hyoung-Joo,Paik, Young-Ki,Kim, Jin Yo American Chemical Society 2017 Journal of proteome research Vol.16 No.12
<P>Human Proteome Project aims to map all human proteins including missing proteins as well as proteoforms with post translational modifications, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). neXtProt and Ensemble databases are usually used to provide curated information on human coding genes. However, to find these proteoforms, we (Chr #11 team) first introduce a streamlined pipeline using customized and concatenated neXtProt and GENCODE originated from Ensemble, with controlled false discovery rate (FDR). Because of large sized databases used in this pipeline, we found more stringent FDR filtering (0.1% at the peptide level and 1% at the protein level) to claim novel findings, such as GENCODE ASVs and missing proteins, from human hippocampus data set (MSV000081385) and ProteomeXchange (PXD007166). Using our next generation proteomic pipeline (nextPP) with neXtProt and GENCODE databases, two missing proteins such as activity-regulated cytoskeleton-associated protein (ARC, Chr 8) and glutamate receptor ionotropic, kainite 5 (GRIK5, Chr 19) were additionally identified with two or more unique peptides from human brain tissues. Additionally, by applying the pipeline to human brain related data sets such as cortex (PXD000067 and PXD000561), spinal cord, and fetal brain (PXD000561), seven GENCODE ASVs such as ACTN4–012 (Chr.19), DPYSL2–005 (Chr.8), MPRIP-003 (Chr.17), NCAM1–013 (Chr.11), EPB41L1–017 (Chr.20), AGAP1–004 (Chr.2), and CPNE5–005 (Chr.6) were identified from two or more data sets. The identified peptides of GENCODE ASVs were mapped onto novel exon insertions, alternative translations at 5′-untranslated region, or novel protein coding sequence. Applying the pipeline to male reproductive organ related data sets, 52 GENCODE ASVs were identified from two testis (PXD000561 and PXD002179) and a spermatozoa (PXD003947) data sets. Four out of 52 GENCODE ASVs such as RAB11FIP5–008 (Chr. 2), RP13–347D8.7–001 (Chr. X), PRDX4–002 (Chr. X), and RP11–666A8.13–001 (Chr. 17) were identified in all of the three samples.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jprobs/2017/jprobs.2017.16.issue-12/acs.jproteome.7b00223/production/images/medium/pr-2017-00223z_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/pr7b00223'>ACS Electronic Supporting Info</A></P>
Chromosome-Centric Human Proteome Study of Chromosome 11 Team
( Heeyoun Hwang ),( Jin Young Kim ),( Jong Shin Yoo ) 한국질량분석학회 2021 Mass spectrometry letters Vol.12 No.3
As a part of the Chromosome-centric Human Proteome Project (C-HPP), we have developed a few algorithms for accurate identification of missing proteins, alternative splicing variants, single amino acid variants, and characterization of function unannotated proteins. We have found missing proteins, novel and known ASVs, and SAAVs using LC-MS/MS data from human brain and olfactory epithelial tissue, where we validated their existence using synthetic peptides. According to the neXtProt database, the number of missing proteins in chromosome 11 shows a decreasing pattern. The development of genomic and transcriptomic sequencing techniques make the number of protein variants in chromosome 11 tremendously increase. We developed a web solution named as SAAvpedia for identification and function annotation of SAAVs, and the SAAV information is automatically transformed into the neXtProt web page using REST API service. For the 73 uPE1 in chromosome 11, we have studied the function annotaion of CCDC90B (NX_Q9GZT6), SMAP (NX_O00193), and C11orf52 (NX_Q96A22).
Heeyoun Hwang,Ju Yeon Lee,Hyun Kyoung Lee,Gun Wook Park,Hoi Keun Jeong,Myeong Hee Moon,Jin Young Kim,Jong Shin Yoo 한국당과학회 2017 한국당과학회 학술대회 Vol.2017 No.01
The characterization of site-specific micro-heterogeneity in glycoprotein is very important for understanding cell biology and disease processes. Vitronectin is well known to be a multi-functional glycoprotein in blood and the extracellular matrix, which is related to hepatocellular carcinoma (HCC). Here, we systematically analyzed the site-specific N-glycopeptides of vitronectin in human plasma by tandem mass spectrometry combined with immunoprecipitation and HILIC enrichment. Vitronectin was purified with immunoprecipitation by monoclonal antibody from plasma and digested to tryptic N-glycopeptides. Then, enrichment with HILIC materials was used, and followed by analysis with nano-LC/MS/MS. The sequences of N-glycopeptides were identified from the mass spectra by high-energy C-trap dissociation (HCD) and collision-induced dissociation (CID). In HCD mode, oxonium ions were used for recognizing glycopeptides and y ions for sequencing the peptide backbone. In CID mode, Y ions were used for characterizing their glycoforms. As a result, total 17 site-specific N-glycopeptides were completely identified at all of three N-glycosylation sites of vitronectin in human plasma, including 12 N-glycopeptides first reported. Finally, we specifically found that three hybrid and four complex glycopeptides of tri-antennary forms with outer-fucosylation increased in HCC human plasma.
Hwang, Heeyoun,Cho, Man-Ho,Bhoo, Seong Hee,Hahn, Tae-Ryong 한국식물생명공학회 2013 Plant biotechnology reports Vol.7 No.3
Leaf starch synthesized during the day for transient storage of photoassimilated carbon is degraded the following night to support respiration and growth in plants. Maltose is a major product of starch degradation, and is exported to the cytosol through the maltose transporter (MEX1). The Arabidopsis mex1 mutant displays growth retardation and an exceptional chlorotic phenotype that is not observed in other mutants demonstrating defective starch synthesis or degradation. Consistent with the chlorotic phenotype, proteomic analysis revealed degeneration of the photosynthetic machinery in mex1, and the down-regulation of essential components for photosynthesis was also observed. The chlorosis observed in mex1 occurs during vegetative growth period under normal growth conditions, which is distinct from general senescence-induced chlorosis. No up-regulation of senescence-related genes was found in the proteomic analysis of mex1, suggesting that the chlorotic process occurring in mex1 is likely distinct from senescence-dependent processes. On the other hand, cellular processes needed to survive stress situations caused by the blocking of maltose export are induced in mex1 by up-regulation of stress-related proteins, such as a germin-like protein and glutathione S-transferase. The increased abundance of heat shock protein 93-V participating in chloroplast biogenesis and rubisco activase, a regulatory protein of photosynthesis, likely reflects an attempt by the mex1 mutant to maintain chloroplast function to survive stress conditions.
Hwang, Heeyoun,Jeong, Ji Eun,Lee, Hyun Kyoung,Yun, Ki Na,An, Hyun Joo,Lee, Bonghee,Paik, Young-Ki,Jeong, Tae Seok,Yee, Gi Taek,Kim, Jin Young,Yoo, Jong Shin American Chemical Society 2018 Journal of proteome research Vol.17 No.12
<P>We performed proteomic analyses of human olfactory epithelial tissue to identify missing proteins using liquid chromatography-tandem mass spectrometry. Using a next-generation proteomic pipeline with a < 1.0% false discovery rate at the peptide and protein levels, we identified 3731 proteins, among which five were missing proteins (P0C7M7, P46721, P59826, Q658L1, and Q8N434). We validated the identified missing proteins using the corresponding synthetic peptides. No olfactory receptor (OR) proteins were detected in olfactory tissue, suggesting that detection of ORs would be very difficult. We also identified 49 and 50 alternative splicing variants mapped at the neXtProt and GENCODE databases, respectively, and 2000 additional single amino acid variants. This data set is available at the ProteomeXchange consortium via PRIDE repository (PXD010025).</P> [FIG OMISSION]</BR>
Hwang, Heeyoun,Lee, Ju Yeon,Lee, Hyun Kyoung,Park, Gun Wook,Jeong, Hoi Keun,Moon, Myeong Hee,Kim, Jin Young,Yoo, Jong Shin Springer-Verlag 2014 Analytical and Bioanalytical Chemistry Vol.406 No.30
<P>The characterization of site-specific microheterogeneity in glycoprotein is very important for understanding cell biology and disease processes. Vitronectin is well known to be a multifunctional glycoprotein in the blood and the extracellular matrix, which is related to hepatocellular carcinoma (HCC). Here, we systematically analyzed the site-specific N-glycopeptides of vitronectin in human plasma by tandem mass spectrometry combined with immunoprecipitation and hydrophilic interaction liquid chromatography (HILIC) enrichment. Vitronectin was purified with immunoprecipitation by monoclonal antibody from plasma and digested to tryptic N-glycopeptides.Then, enrichment with HILIC materials was used and followed by analysis with nano-LC/MS/MS. The sequences of N-glycopeptides were identified from the mass spectra by high-energy C-trap dissociation (HCD) and collision-induced dissociation (CID). In HCD mode, oxonium ions were used for recognizing glycopeptides and y ions for sequencing the peptide backbone. In CID mode, Y ions were used for characterizing their glycoforms. As a result, a total of 17 site-specific N-glycopeptides were completely identified in all of the three N-glycosylation sites of vitronectin in human plasma, including 12 N-glycopeptides first reported. Finally, we specifically found that three hybrid and four complex glycopeptides of triantennary forms with outer fucosylation increased in HCC human plasma.</P>