C-HPP Papers
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2017 JPR Special Issue
- Paik, Y. K. et al. (2017) Progress and Future Direction of Chromosome-Centric Human Proteome Project. J. Proteome Res., 16, 4253-4258.
- Meyfour, A. et al. (2017) Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development. J. Proteome Res., 16, 4259-4272.
- Tholey, A. et al. (2017) We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project. J. Proteome Res., 16, 4273-4280.
- Omenn, G. S. et al. (2017) Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. J. Proteome Res., 16, 4281-4287.
- Deutsch, E. W. et al. (2017) Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. J. Proteome Res., 16, 4288-4298.
- Schwenk, J. M. et al. (2017) The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J. Proteome Res., 16, 4299-4310.
- Poverennaya, E. V. et al. (2017) Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J. Proteome Res., 16, 4311-4318.
- Alberio, T. et al. (2017) Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative. J. Proteome Res., 16, 4319-4329.
- Li, S. et al. (2017) Digging More Missing Proteins Using an Enrichment Approach with ProteoMiner. J. Proteome Res., 16, 4330-4339.
- Carapito, C. et al. (2017) Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods. J. Proteome Res., 16, 4340-4351.
- Wang, Y. et al. (2017) Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J. Proteome Res., 16, 4352-4363.
- Peng, X. et al. (2017) Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer. J. Proteome Res., 16, 4364-4373.
- Guruceaga, E. et al. (2017) Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. J. Proteome Res., 16, 4374-4390.
- Meyfour, A. et al. (2017) Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation. J. Proteome Res., 16, 4391-4402.
- Elguoshy, A. et al. (2017) Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy. J. Proteome Res., 16, 4403-4414.
- Choong, W. K. et al. (2017) Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome. J. Proteome Res., 16, 4415-4424.
- Hwang, H. et al. (2017) Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases. J. Proteome Res., 16, 4425-4434.
- Cho, J. Y. et al. (2017) Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification. J. Proteome Res., 16, 4435-4445.
- Zhao, P. et al. (2017) Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage. J. Proteome Res., 16, 4446-4454.
- Na, K. et al. (2017) Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins. J. Proteome Res., 16, 4455-4467.
- Zhang, W. et al. (2017) Detergent-Insoluble Proteome Analysis Revealed Aberrantly Aggregated Proteins in Human Preeclampsia Placentas. J. Proteome Res., 16, 4468-4480.
- Velásquez, E. et al. (2017) Synaptosomal Proteome of the Orbitofrontal Cortex from Schizophrenia Patients Using Quantitative Label-Free and iTRAQ-Based Shotgun Proteomics. J. Proteome Res., 16, 4481-4494.
- Togayachi, A. et al. (2017) Glycobiomarker, Fucosylated Short-Form Secretogranin III Levels Are Increased in Serum of Patients with Small Cell Lung Carcinoma. J. Proteome Res., 16, 4495-4505.
- Mora, M. I. et al. (2017) Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. J. Proteome Res., 16, 4506-4514.
- Zhang, S. et al. (2017) Profiling B-Type Natriuretic Peptide Cleavage Peptidoforms in Human Plasma by Capillary Electrophoresis with Electrospray Ionization Mass Spectrometry. J. Proteome Res., 16, 4515-4522.
- Zhou, J. Y. et al. (2017) Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. J. Proteome Res., 16, 4523-4530.
- Mohamedali, A. et al. (2017) Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence? J. Proteome Res., 16, 4531-4535.
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2016 JPR Special Issue
- Paik, Y. K. et al. (2016) Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV. J. Proteome Res., 15, 3945-3950.
- Omenn, G. S. et al. (2016) Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J. Proteome Res., 15, 3951-3960.
- Deutsch, E. W. et al. (2016) Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. J. Proteome Res., 15, 3961-3970.
- Duek, P. et al. (2016) Missing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status. J. Proteome Res., 15, 3971-3978.
- Van Eyk, J. E. et al. (2016) Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. J. Proteome Res., 15, 3979-3987.
- Wei, W. et al. (2016) Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer. J. Proteome Res., 15, 3988-3997.
- Vandenbrouck, Y. et al. (2016) Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J. Proteome Res., 15, 3998-4019.
- Zhao, M. et al. (2016) Searching Missing Proteins Based on the Optimization of Membrane Protein Enrichment and Digestion Process. J. Proteome Res., 15, 4020-4029.
- Poverennaya, E. V. et al. (2016) State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells. J. Proteome Res., 15, 4030-4038.
- Kopylov, A. T. et al. (2016) Targeted Quantitative Screening of Chromosome 18 Encoded Proteome in Plasma Samples of Astronaut Candidates. J. Proteome Res., 15, 4039-4046.
- Guo, J. et al. (2016) Drug Resistance in Colorectal Cancer Cell Lines is Partially Associated with Aneuploidy Status in Light of Profiling Gene Expression. J. Proteome Res., 15, 4047-4059.
- Guo, J. et al. (2016) Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP. J. Proteome Res., 15, 4060-4072.
- Weiland, F. et al. (2016) Novel IEF Peptide Fractionation Method Reveals a Detailed Profile of N-Terminal Acetylation in Chemotherapy-Responsive and -Resistant Ovarian Cancer Cells. J. Proteome Res., 15, 4073-4081.
- Park, G. W. et al. (2016) Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate. J. Proteome Res., 15, 4082-4090.
- Deutsch, E. W. et al. (2016) Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. J. Proteome Res., 15, 4091-4100.
- Garin-Muga, A. et al. (2016) Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. J. Proteome Res., 15, 4101-4115.
- Kim, J. W. et al. (2016) gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides. J. Proteome Res., 15, 4116-4125.
- Lam, M. P. et al. (2016) Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. J. Proteome Res., 15, 4126-4134.
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2015 JPR Special Issue
- Paik, Y. K. et al. (2015) Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J. Proteome Res., 14, 3409-3414.
- Horvatovich, P. et al. (2015) Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3415-3431.
- Jayaram, S. et al. (2015) Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective. J. Proteome Res., 14, 3432-3440.
- Horvatovich, P. et al. (2015) In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J. Proteome Res., 14, 3441-3451.
- Omenn, G. S. et al. (2015) Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J. Proteome Res., 14, 3452-3460.
- Deutsch, E. W. et al. (2015) State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. J. Proteome Res., 14, 3461-3473.
- Vakilian, H. et al. (2015) DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J. Proteome Res., 14, 3474-3483.
- Li, H. D. et al. (2015) Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. J. Proteome Res., 14, 3484-3491.
- Jangravi, Z. et al. (2015) Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J. Proteome Res., 14, 3492-3502.
- Rengaraj, D. et al. (2015) Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions. J. Proteome Res., 14, 3503-3518.
- Menon, R. et al. (2015) Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. J. Proteome Res., 14, 3519-3529.
- Díez, P. et al. (2015) Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3530-3540.
- Tay, A. P. et al. (2015) Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J. Proteome Res., 14, 3541-3554.
- Woo, S. et al. (2015) Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J. Proteome Res., 14, 3555-3567.
- Eckhard, U. et al. (2015) The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. J. Proteome Res., 14, 3568-3582.
- Zhang, Y. et al. (2015) Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins. J. Proteome Res., 14, 3583-3594.
- Ahmadi Rastegar, D. et al. (2015) Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients. J. Proteome Res., 14, 3595-3605.
- Jumeau, F. et al. (2015) Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3606-3620.
- Carapito, C. et al. (2015) Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14. J. Proteome Res., 14, 3621-3634.
- Fan, Y. et al. (2015) Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected. J. Proteome Res., 14, 3635-3644.
- Yang, L. et al. (2015) Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J. Proteome Res., 14, 3645-3657.
- Kitata, R. B. et al. (2015) Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. J. Proteome Res., 14, 3658-3669.
- Hoover, H. et al. (2015) Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers. J. Proteome Res., 14, 3670-3679.
- Su, N. et al. (2015) Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples. J. Proteome Res., 14, 3680-3692.
- Chen, Y. et al. (2015) Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J. Proteome Res., 14, 3693-3709.
- Jeong, S. K. et al. (2015) GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 14, 3710-3719.
- Yang, S. et al. (2015) CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets. J. Proteome Res., 14, 3720-3728.
- Krasnov, G. S. et al. (2015) PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics. J. Proteome Res., 14, 3729-3737.
- Tabas-Madrid, D. et al. (2015) Proteogenomics Dashboard for the Human Proteome Project. J. Proteome Res., 14, 3738-3749.
- Dong, Q. et al. (2015) Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J. Proteome Res., 14, 3750-3761.
- Panwar, B. et al. (2015) MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. J. Proteome Res., 14, 3762-3767.
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2014 JPR Special Issue
- Paik, Y. K. et al. (2014) Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J. Proteome Res., 13, 1-4.
- Horvatovich, P. et al. (2014) Proteomic studies related to genetic determinants of variability in protein concentrations. J. Proteome Res., 13, 5-14.
- Lane, L. et al. (2014) Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J. Proteome Res., 13, 15-20.
- Woo, S. et al. (2014) Proteogenomic database construction driven from large scale RNA-seq data. J. Proteome Res., 13, 21-28.
- Teo, G. et al. (2014) PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation. J. Proteome Res., 13, 29-37.
- Chang, C. et al. (2014) Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP. J. Proteome Res., 13, 38-49.
- Zhong, J. et al. (2014) Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J. Proteome Res., 13, 50-59.
- Farrah, T. et al. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J. Proteome Res., 13, 60-75.
- Islam, M. T. et al. (2014) Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome. J. Proteome Res., 13, 76-83.
- Pang, C. N. et al. (2014) Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J. Proteome Res., 13, 84-98.
- Wang, D. et al. (2014) CAPER 2.0: an interactive, configurable, and extensible workflow-based platform to analyze data sets from the Chromosome-centric Human Proteome Project. J. Proteome Res., 13, 99-106.
- Higdon, R. et al. (2014) MOPED enables discoveries through consistently processed proteomics data. J. Proteome Res., 13, 107-113.
- Zhang, C. et al. (2014) Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1. J. Proteome Res., 13, 114-125.
- Liu, Y. et al. (2014) Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications. J. Proteome Res., 13, 126-136.
- Ahn, J. M. et al. (2014) Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. J. Proteome Res., 13, 137-146.
- Martins-de-Souza, D. et al. (2014) Deciphering the human brain proteome: characterization of the anterior temporal lobe and corpus callosum as part of the Chromosome 15-centric Human Proteome Project. J. Proteome Res., 13, 147-157.
- Segura, V. et al. (2014) Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. J. Proteome Res., 13, 158-172.
- Shargunov, A. V. et al. (2014) Tissue-specific alternative splicing analysis reveals the diversity of chromosome 18 transcriptome. J. Proteome Res., 13, 173-182.
- Ponomarenko, E. A. et al. (2014) Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013. J. Proteome Res., 13, 183-190.
- Lichti, C. F. et al. (2014) Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J. Proteome Res., 13, 191-199.
- Wang, Q. et al. (2014) Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines. J. Proteome Res., 13, 200-211.
- Menon, R. et al. (2014) Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J. Proteome Res., 13, 212-227.
- Sheynkman, G. M. et al. (2014) Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J. Proteome Res., 13, 228-240.
- Song, C. et al. (2014) Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. J. Proteome Res., 13, 241-248.
- Peng, M. et al. (2014) Identification of enriched PTM crosstalk motifs from large-scale experimental data sets. J. Proteome Res., 13, 249-259.
- Edwards, A. V. et al. (2014) Spatial and temporal effects in protein post-translational modification distributions in the developing mouse brain. J. Proteome Res., 13, 260-267.
- Leng, L. et al. (2014) A proteomics strategy for the identification of FAT10-modified sites by mass spectrometry. J. Proteome Res., 13, 268-276.
- Sethi, M. K. et al. (2014) Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines. J. Proteome Res., 13, 277-288.
- Gbormittah, F. O. et al. (2014) Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform. J. Proteome Res., 13, 289-299.
- Kiel, C. et al. (2014) Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. J. Proteome Res., 13, 300-313.
- Aquino, P. F. et al. (2014) Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer. J. Proteome Res., 13, 314-320.
- Fujimoto, G. M. et al. (2014) Accounting for population variation in targeted proteomics. J. Proteome Res., 13, 321-323.
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2013 JPR Special Issue
- Marko-Varga, G. et al. (2013) A first step toward completion of a genome-wide characterization of the human proteome. J. Proteome Res., 12, 1-5.
- Jangravi, Z. et al. (2013) A fresh look at the male-specific region of the human Y chromosome. J. Proteome Res., 12, 6-22.
- Aebersold, R. et al. (2013) The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J. Proteome Res., 12, 23-27.
- Huhmer, A. F. et al. (2013) The chromosome-centric human proteome project: a call to action. J. Proteome Res., 12, 28-32.
- Chen, L. C. et al. (2013) Decoding the disease-associated proteins encoded in the human chromosome 4. J. Proteome Res., 12, 33-44.
- Liu, S. et al. (2013) A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J. Proteome Res., 12, 45-57.
- Yamamoto, T. et al. (2013) Integrated view of the human chromosome X-centric proteome project. J. Proteome Res., 12, 58-61.
- Imanishi, T. et al. (2013) Full-length transcriptome-based H-InvDB throws a new light on chromosome-centric proteomics. J. Proteome Res., 12, 62-66.
- Wu, S. et al. (2013) First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon. J. Proteome Res., 12, 67-80.
- Zhang, Y. et al. (2013) Proteome atlas of human chromosome 8 and its multiple 8p deficiencies in tumorigenesis of the stomach, colon, and liver. J. Proteome Res., 12, 81-88.
- Fanayan, S. et al. (2013) Chromosome 7-centric analysis of proteomics data from a panel of human colon carcinoma cell lines. J. Proteome Res., 12, 89-96.
- Kwon, K. H. et al. (2013) Chromosome 11-centric human proteome analysis of human brain hippocampus tissue. J. Proteome Res., 12, 97-105.
- Jeong, S. K. et al. (2013) GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J. Proteome Res., 12, 106-111.
- Segura, V. et al. (2013) Spanish human proteome project: dissection of chromosome 16. J. Proteome Res., 12, 112-122.
- Zgoda, V. G. et al. (2013) Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J. Proteome Res., 12, 123-134.
- Nilsson, C. L. et al. (2013) Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. J. Proteome Res., 12, 135-150.
- Wang, Q. et al. (2013) Qualitative and quantitative expression status of the human chromosome 20 genes in cancer tissues and the representative cell lines. J. Proteome Res., 12, 151-161.
- Farrah, T. et al. (2013) The state of the human proteome in 2012 as viewed through PeptideAtlas. J. Proteome Res., 12, 162-171.
- Goode, R. J. et al. (2013) The proteome browser web portal. J. Proteome Res., 12, 172-178.
- Guo, F. et al. (2013) CAPER: a chromosome-assembled human proteome browsER. J. Proteome Res., 12, 179-186.
- Peng, Y. et al. (2013) Top-down targeted proteomics for deep sequencing of tropomyosin isoforms. J. Proteome Res., 12, 187-198.
- Maurer, A. et al. (2013) A periodate-cleavable linker for functional proteomics under slightly acidic conditions: application for the analysis of intracellular aspartic proteases. J. Proteome Res., 12, 199-207.
- Muraoka, S. et al. (2013) In-depth membrane proteomic study of breast cancer tissues for the generation of a chromosome-based protein list. J. Proteome Res., 12, 208-213.
- Yamana, R. et al. (2013) Rapid and deep profiling of human induced pluripotent stem cell proteome by one-shot NanoLC-MS/MS analysis with meter-scale monolithic silica columns. J. Proteome Res., 12, 214-221.
- Percy, A. J. et al. (2013) Standardized protocols for quality control of MRM-based plasma proteomic workflows. J. Proteome Res., 12, 222-233.
- Mortstedt, H. et al. (2013) Screening method using selected reaction monitoring for targeted proteomics studies of nasal lavage fluid. J. Proteome Res., 12, 234-247.
- Malerod, H. et al. (2013) Comprehensive profiling of N-linked glycosylation sites in HeLa cells using hydrazide enrichment. J. Proteome Res., 12, 248-259.
- Zhou, H. et al. (2013) Toward a comprehensive characterization of a human cancer cell phosphoproteome. J. Proteome Res., 12, 260-271.
- Lavallee-Adam, M. et al. (2013) Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. J. Proteome Res., 12, 272-281.
- Buanne, P. et al. (2013) Characterization of carbonic anhydrase IX interactome reveals proteins assisting its nuclear localization in hypoxic cells. J. Proteome Res., 12, 282-292.
- Gaudet, P. et al. (2013) neXtProt: organizing protein knowledge in the context of human proteome projects. J. Proteome Res., 12, 293-298.
- Danielsson, F. et al. (2013) RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins. J. Proteome Res., 12, 299-307.
- Meding, S. et al. (2013) Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. J. Proteome Res., 12, 308-315.
- Wu, Y. et al. (2013) Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. J. Proteome Res., 12, 316-327.
- Xiao, C. L. et al. (2013) Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information. J. Proteome Res., 12, 328-335.
- Sharma, A. et al. (2013) Identification of potential universal vaccine candidates against group A Streptococcus by using high throughput in silico and proteomics approach. J. Proteome Res., 12, 336-346.
- Maris, M. et al. (2013) Role of the saturated nonesterified fatty acid palmitate in beta cell dysfunction. J. Proteome Res., 12, 347-362.
- Ye, Y. et al. (2013) Quantitative proteomics by amino acid labeling in foot-and-mouth disease virus (FMDV)-infected cells. J. Proteome Res., 12, 363-377.
- Kliemt, S. et al. (2013) Sulfated hyaluronan containing collagen matrices enhance cell-matrix-interaction, endocytosis, and osteogenic differentiation of human mesenchymal stromal cells. J. Proteome Res., 12, 378-389.
- Sun, D. et al. (2013) Quantitative proteome of medulla oblongata in spontaneously hypertensive rats. J. Proteome Res., 12, 390-395.
- Klatt, S. et al. (2013) Production of glycosylated soluble amyloid precursor protein alpha (sAPPalpha) in Leishmania tarentolae. J. Proteome Res., 12, 396-403.
- Fujita, T. et al. (2013) Proteomic analysis of the royal jelly and characterization of the functions of its derivation glands in the honeybee. J. Proteome Res., 12, 404-411.
- Torsetnes, S. B. et al. (2013) Digging deeper into the field of the small cell lung cancer tumor marker ProGRP: a method for differentiation of its isoforms. J. Proteome Res., 12, 412-420.
- Cirillo, F. et al. (2013) Molecular mechanisms of selective estrogen receptor modulator activity in human breast cancer cells: identification of novel nuclear cofactors of antiestrogen-ERα complexes by interaction proteomics. J. Proteome Res., 12, 421-431.
- Lee, J. Y. et al. (2013) Proteomic and transcriptional analysis of Lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR. J. Proteome Res., 12, 432-443.
- Adamczyk, B. et al. (2013) Characterization of fibrinogen glycosylation and its importance for serum/plasma N-glycome analysis. J. Proteome Res., 12, 444-454.
- Hrabakova, R. et al. (2013) Cancer cell resistance to aurora kinase inhibitors: identification of novel targets for cancer therapy. J. Proteome Res., 12, 455-469.
- Pechlivanis, A. et al. (2013) 1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum. J. Proteome Res., 12, 470-480.
- O'Sullivan, A. et al. (2013) Metabolomics of cerebrospinal fluid from humans treated for rabies. J. Proteome Res., 12, 481-490.
- Huang, M. et al. (2013) Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics. J. Proteome Res., 12, 491-504.
- Zhang, T. et al. (2013) Identification of potential biomarkers for ovarian cancer by urinary metabolomic profiling. J. Proteome Res., 12, 505-512.
- Tan, Y. et al. (2013) Deciphering the differential toxic responses of Radix aconiti lateralis praeparata in healthy and hydrocortisone-pretreated rats based on serum metabolic profiles. J. Proteome Res., 12, 513-524.
- Strakova, E. et al. (2013) Systems insight into the spore germination of Streptomyces coelicolor. J. Proteome Res., 12, 525-536.
- Huang, C. et al. (2013) Metabolic influence of acute cyadox exposure on Kunming mice. J. Proteome Res., 12, 537-545.
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C-HPP Related Papers
- Ruiz-Romero, C. et al. (2015) The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases. J Proteomics, , .
- Guruceaga, E. et al. (2015) Prediction of a Missing Protein Expression Map in the Context of the Human Proteome Project. J. Proteome Res., , .
- Lichti, C. F. et al. (2015) Systematic identification of single amino Acid variants in glioma stem-cell-derived chromosome 19 proteins. J. Proteome Res., 14, 778-786.
- Nilsson, C. L. et al. (2015) Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome. J. Proteome Res., 14, 603-608.
- Manda, S. S. et al. (2014) Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project. J. Proteome Res., 13, 3166-3177.
- Chaiyarit, S. et al. (2014) Chromosome-centric Human Proteome Project (C-HPP): Chromosome 12. J. Proteome Res., 13, 3160-3165.
- Gupta, M. K. et al. (2014) Chromosome-centric human proteome project: deciphering proteins associated with glioma and neurodegenerative disorders on chromosome 12. J. Proteome Res., 13, 3178-3190.
- Pinto, S. M. et al. (2014) Functional annotation of proteome encoded by human chromosome 22. J. Proteome Res., 13, 2749-2760.
- Lange, P. F. et al. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res., 13, 2028-2044.
- Stadler, C. et al. (2014) RNA- and antibody-based profiling of the human proteome with focus on chromosome 19. J. Proteome Res., 13, 2019-2027.
- Alm, T. et al. (2014) A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia. J. Proteome Res., 13, 1669-1676.
- Ponomarenko, E. et al. (2014) The chromosome-centric human proteome project at FEBS Congress. Proteomics, 14, 147-152.
- Malm, J. et al. (2013) Blood plasma reference material: a global resource for proteomic research. J. Proteome Res., 12, 3087-3092.
- Ranganathan, S. et al. (2013) Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach. J. Proteome Res., 12, 2504-2510.
- Lee, H. J. et al. (2013) Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project. J. Proteome Res., 12, 2458-2466.
- Fagerberg, L. et al. (2013) Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J. Proteome Res., 12, 2439-2448.
- Shiromizu, T. et al. (2013) Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-centric Human Proteome Project. J. Proteome Res., 12, 2414-2421.
- Fanayan, S. et al. (2013) Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405. J. Proteome Res., 12, 1732-1742.
- Paik, Y. K. and Hancock, W. S. (2012) Uniting ENCODE with genome-wide proteomics. Nat. Biotechnol. 30, 1065-1067.
- Paik,Y. et al. (2012) The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol, 30, 221-3.
- Archakov, A. et al. (2011) Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18. Proteomics, 11, 1853-1856.
- Hancock,W. et al. (2011) Proteomics, human proteome project, and chromosomes. J Proteome Res, 10, 210.
- Editorial (2010) A gene-centric human proteome project: HUPO-the Human Proteome organization. Mol Cell Proteomics, 9, 427-9.
- Berglund,L. et al. (2008) A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics, 7, 2019-27.
