Human liver tissue lysate was analyzed by multiple technical routes combining with mass spectrometry and the data was open as Liverbase 1.0. In Liverbase 2.0, we performed organelle proteome of adult human liver, by which the scale of data was enlarged further. To combine with human liver organellar proteome (HLOP) dataset, all MS/MS raw files of the Human Liver Proteome (HLP) dataset were reanalyzed using the same database search process for HLOP dataset as described above. We integrated these two datasets to get an overall view of proteins expressed in human liver. Finally, a total of 12,168 high-confidence proteins with 70,000 non-redundancy peptide sequences were recorded in 2.0 datasets, which was corresponded to 9,885 protein coding genes.

  The sample collection was complied with the regulations of Ethics Committee of the Chinese Human Liver Proteome Project. All samples were collected from volunteers of the Chinese Han nationality who underwent hepatic hemangioma resection (neoplastic lesions were less than 5 cm in diameter). The donors were given a comprehensive clinical test, including alanine aminotransferase, aspartate aminotransferase, g-glutmyl transferase, alkaline phosphatase, bilirubin, albumin, prothrombin time and alpha-feto protein, to ensure the donors were free from viral hepatitis, autoimmune liver disease, cystic liver disease, fatty liver disease, etc. All donors were given informed consent before surgery. The tissue was excised 2 cm away from tumor and collected immediately. The organelle isolation was followed by previous report [Song Y, Hao Y, Sun A, Li T, Li W, Guo L, Yan Y, Geng C, Chen N, Zhong F, Wei H, Jiang Y, He F. Sample preparation project for the subcellular proteome of mouse liver. Proteomics. 2006 6(19):5269-77]

  The human International Protein Index (IPI) database (version 3.24) was downloaded and a decoy strategy was established for database searching. All raw files were searched against the concatenated target–decoy database using a local Turbo SEQUEST v.27 server. The BNP model was applied to all resulted peptide-spectra matches to get the identified peptides with a 5% FDR measured by the reversed hits. The false discovery rates (FDRs) are estimated by the formula: FDREst= Nd/Nt. Nt and Nd are the number of target and decoy matches, respectively, which pass the predetermined filter rules. The minimal protein lists were assembled according to the parsimony principle. The representative protein of a given group in the final list was defined based on database source and sequence length.

  A modified semi-quantitation method based on spectral count (SC) was used to in quantitative estimation of human liver organelle datasets. SC value for each protein was normalized by the theoretical peptide number and the same protein from different batch was normalized by total spectrum number of identified peptide of each experiment. The normalized SC values, also called SCIN (spectral count index normalized), of 4,961 and 4,306 proteins were calculated for LTQ and LCQ data respectively.

  To obtain the new subcellular localizations identified in this study, we intergrate our data with the known subcelluar localization information with high quality in the public databases, such as Swiss-Prot, GOA, MitoP2, HPA, etc. To ensure the quality of the data we referenced, proteins with uncertain annotation in Swiss-Prot, such as “By similarity” “Potential” or “Probable” were removed; subcellular annotations with experimental evidence in GOA, such as “EXP (Inferred from Experiment)”, “IC (Inferred by Curator)”, “IDA (Inferred from Direct Assay)”, “IGI (Inferred from Genetic Interaction)”, “IMP (Inferred from Mutant Phenotype)”, “IPI (Inferred from Physical Interaction) ”, “TAS (Traceable Author Statement) ” were remained; subcellular identifications in HPA with “Supportive” or “High” reliability were remained.

  If you use Liverbase in any published work, please cite the following reference: Sun, A.; Jiang, Y.; Wang, X.; Liu, Q.; Zhong, F.; He, Q.; Guan, W.; Li, H.; Sun, Y.; Shi, L.; Yu, H.; Yang, D.; Xu, Y.; Song, Y.; Tong, W.; Li, D.; Lin, C. L.; Hao, Y.; Geng, C.; Yun, D.; Zhang, X.; Yuan, X.; Chen, P.; Zhu, Y.; Li, Y.; Liang, S.; Zhao, X. H.; Liu, S.; He, F., Liverbase: a comprehensive view of human liver biology. J Proteome Res 2009.

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