The neXt-50 Challenge The neXt-50 Challenge Chromosome 1 PIC Leaders: Ping Xu Major lab members or partners contributing to the next-MP50: Ping Xu, Fuchu He, Yao Zhang, Feng Xu, Yanchang Li, Wei Wei, Yihao Wang, Xuehui Peng, Yang Chen, Shu Liu, Suzhen Li, Jinshuai Sun, Cuitong He, and Jiahui Shi Status of the Chromosome “parts list” for your Chromosome: According to the newest neXtProt (2018-01) dataset, we've updated the protein PE distribution of Ch1. A) Titles and authors of papers submitted to the 2018 JPR SI and their status (eg in press, or under revision). 1) Jinshuai Sun, Jiahui Shi, Yihao Wang, Yang Chen, Yanchang Li, Degang Kong, Lei Chang, Fengsong Liu, Zhitang Lv, Yue Zhou, Fuchu He, Yao Zhang, Ping Xu. Multi-Proteases Combined with High-pH Reverse- Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue (pr-2018-00397q, revised) 2) Cuitong He, Jiahui Shi, Jinshuai Sun, Yihao Wang, Jialing Zhao, Shujia Wu, Yanchang Li, Lei Chang, Huiying Gao, Fengsong Liu, Zhitang Lv, Junzhu Wu, Fuchu He, Yao Zhang, Ping Xu. Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a Mirror Protease Strategy (pr-2018-00398m, revised) B) Titles and authors of papers published in the 2017 JPR SI. 1) Yihao Wang, Yang Chen, Yao Zhang, Wei Wei, Yanchang Li, Tao Zhang, Fuchu He, Yue Gao, Ping Xu. Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. 2017, 16(12): 4352- 4363. 2) Xuehui Peng, Feng Xu, Shu Liu, Suzhen Li, Qingbo Huang, Lei Chang, Lei Wang, Xin Ma, Fuchu He, Ping Xu. Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer. 2017, 16(12): 4364-4373. C) Titles and authors of other HPP relevant papers submitted elsewhere in the past 2 years. 1) Cuitong He, Chenxi Jia, Yao Zhang, and Ping Xu. Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae. J. Proteome Res. 17, 7, 2335-2344 D) How many PE1-found MPs since HUPO-2017 has your chromosome group reported in papers? C-HPP 2018-10-22 1 The neXt-50 Challenge According to the newest neXtProt (2018-01) dataset, nineteen MPs has been listed as PE1 proteins since HUPO-2017, 15 proteins were from Siqi Liu lab, three proteins from Ping Xu lab, and one protein from Gong Zhang lab. E) How many PE1-found MPs since HUPO-2017 are now in NeXt-Prot as PE1 proteins? Please check each of your MPs that you reported in the JPR SI. According to the newest neXtProt (2018-01) dataset, three MPs has been listed as PE1 proteins since HUPO- 2017, two proteins (P0DMU9 and P0C5Z0) were from Wang, et al, and one protein (P81133) was from Peng, et al work. F) How many candidate MPs found, but not meeting the guidelines 2.1? (Please state number of peptides identified, their length, and biological replicates found in). In our pr-2018-00397q work, we also identified the other 39 MP candidates. It is worth to mention that we verified 4 MP candidates with one peptide containing more than 9 AA residues and another one containing only 8 AA residues, which is slightly lower than the criteria listed by C-HPP 2.1. In addition, we showed the high quality spectra of the 35 MP candidates with more than 1 unique peptides in supplementary figures (at least one peptide with more than 9 AA residues), which can be verified by peptide synthesis or other strategies. Among of these 39 MP candidates, 34 proteins were identified by at least two proteases digesting samples, and the other 5 proteins were identified by unique protease digestion. In our pr-2018-00398m work, we also identified the other 4 MP candidates (Q0VDE8, Q2VIQ3, P0DMW4, Q8TBE1) with one unique peptide from LMW-enriching proteins, which showed high quality spectra and were verified by peptide synthesis. Among these 4 MP candidates, P0DMW4 was identified from the combination strategy of trypsin digestion and Gel-separating, and the other three proteins were from a single enriching strategy. G) Any significant clinical or other successes are MP that you wish us to consider highlighting in the report. The aim of pr-2018-00397q study was to dig more MPs by multi-protease method combined with high-pH RP separation based on large-scale proteomics. Surprisingly, we totally identified as many as 11,558 proteins from the pooled testis samples with three individuals, which is the largest proteome dataset for single human tissue sample so far, suggesting the huge effort we put on the C-HPP project this year. Taking advantage of this large dataset, we totally identified 100 MP candidates and verified 14 MPs. IPA analysis of these newly identified 14 MPs showed that 10 proteins were closely associated with liver disease and might be used for screening potential biomarkers for liver disease. The aim of pr-2018-00398m study was to search small MP candidates based on LMW protein enriching strategy. To enrich these LMW proteins, we tried four different enriching strategies. To increase the identification credibility of LMW proteins, we utilized Trypsin and LysargiNase. Totally, we identified 4,063 proteins, which is a big proteome dataset specifically for the enriched LMW proteins. Among them, we identified seven MP candidates. The molecular weight of six MP candidates were lower than 40 kDa and four MP candidates were lower than 20 kDa. Importantly, these MP candidates with LWM can only be identified by the enriched LMW fractions but not in the largest testis proteome dataset, implying the efficiency of the enriching strategies applied in this study. This is the first time to introduce both of LMW proteins and mirror protease for testis sample in C- HPP, which may help to widespread use in the near future. Chromosome 2 PIC Leaders: Lydie Lane Major lab members or partners contributing to the next-MP50: C-HPP 2018-10-22 2 The neXt-50 Challenge Paula Duek (SIB/University of Geneva) Alain Gateau (SIB/University of Geneva) Thibault Robin (SIB/University of Geneva) Frédérique Lisacek (SIB/University of Geneva) Markus Mueller (SIB Lausanne) Amos Bairoch (SIB/University of Geneva) Charlotte Macron (Nestlé Institute of Health Sciences) Antonio Nunez-Galindo (Nestlé Institute of Health Sciences) Loïc Dayon (Nestlé Institute of Health Sciences) Status of the Chromosome “parts list” for your Chromosome: There were 130 MP on chr 2 in 2017, now only 98. A) Titles and authors of papers submitted to the 2018 JPR SI and their status (eg in press, or under revision). Related to the next-MP50 challenge: Macron C, Lane L, Núñez Galindo A, Dayon L., Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res. 2018 Aug 31. doi: 10.1021/acs.jproteome.8b00300. [Epub ahead of print] PMID: 30124047 Macron C, Lane L, Núñez Galindo A, Dayon L., Identification of Missing Proteins in Normal Human Cerebrospinal Fluid. J Proteome Res. 2018 Aug 17. doi: 10.1021/acs.jproteome.8b00194. [Epub ahead of print] PMID: 30106588 Robin T, Bairoch A, Müller M, Lisacek F, Lane L., Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project. J Proteome Res. 2018 Sep 17. doi: 10.1021/acs.jproteome.8b00392. [Epub ahead of print] PMID: 30175587 Related to the uPE1 challenge: Duek P, Gateau A, Bairoch A, Lane L., Exploring the uncharacterized human proteome using neXtProt. J Proteome Res. 2018 Sep 7. doi: 10.1021/acs.jproteome.8b00537. [Epub ahead of print] PMID: 30191714 C-HPP 2018-10-22 3 The neXt-50 Challenge Paik Y-K, Lane L, Kawamura T, Chen Y-J, Cho J-Y, LaBaer J, Yoo J S, Domont G, Corrales F, Omenn G, Arcjakov A, Encarnación-Guevara S, Liu S, Salekdeh G H, Cho J-Y, Kim C-Y, Overall C, Launching the C-HPP pilot project for functional characterization of identified proteins with no known function, in revision Other papers related to HPP Monti C, Lane L, Fasano M, Alberio T, An update of the functional mitochondrial human proteome network, J Proteome Res. 2018 Sep 19. doi: 10.1021/acs.jproteome.8b00447. [Epub ahead of print] PMID: 302303 Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res. 2018 Aug 23. doi: 10.1021/acs.jproteome.8b00441. [Epub ahead of print] PMID: 30099871 B) Titles and authors of papers published in the 2017 JPR SI. Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Fréour T, Vandenbrouck Y, Lane L, Pineau C., Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody- based Methods. J Proteome Res. 2017 Dec 1;16(12):4340-4351. doi: 10.1021/acs.jproteome.7b00374. Epub 2017 Sep 26. PMID: 28891297 Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW., Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. J Proteome Res. 2017 Dec 1;16(12):4281-4287. doi: 10.1021/acs.jproteome.7b00375. Epub 2017 Oct 9. PMID: 28853897 C) Titles and authors of other HPP relevant papers submitted elsewhere in the past 2 years. Schaeffer M, Gateau A, Teixeira D, Michel PA, Zahn-Zabal M, Lane L., The neXtProt peptide uniqueness checker: a tool for the proteomics community. Bioinformatics. 2017 Nov 1;33(21):3471-3472. doi: 10.1093/bioinformatics/btx318.