PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering7091https://pax-db.org/dataset/7091/1004366984mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Bombyx mori cocoon has a multi-layer structure that provides optimal protection for silkworm pupa. Research on the mechanical properties of the multi-layer structure revealed structure-property relationships of the cocoon. Here, we investigated the protein components of the B. mori cocoon in terms of its multi-layer structure. Liquid chromatography-tandem mass spectrometry identified 286 proteins from the multiple cocoon layers. In addition to fibroins and sericins, we identified abundant protease inhibitors, seroins and proteins of unknown function. By comparing protein abundance across layers, we found that the outermost layer contained more sericin1 and protease inhibitors and the innermost layer had more seroin1. As many as 36 protease inhibitors were identified in cocoons, showing efficient inhibitory activities against a fungal protease. Thus, we propose that more abundant protease inhibitors in the outer cocoon layers may provide better protection for the cocoon. This study increases our understanding of the multi-layer mechanism of cocoons, and helps clarify the biological characteristics of cocoons. The data have been deposited to the ProteomeXchange with identifier PXD001469.Comparative proteome analysis of multi-layer cocoon of the silkworm, Bombyx mori.Zhang Yan Y, Zhao Ping P, Dong Zhaoming Z, Wang Dandan D, Guo Pengchao P, Guo Xiaomeng X, Song Qianru Q, Zhang Weiwei W, Xia Qingyou Q0falseBmori - Cocoon, SC (Zhangetal.,plosone2015)abundance based on Spectral counting, Interaction consistency score: 1.0, Coverage: 22015100436698425860555H9J4M4_BOMMOH9JBP6_BOMMOH9JC16_BOMMOH9IZF9_BOMMOH9IS19_BOMMOH9JTP8_BOMMOE5EVW3_BOMMOLYS_BOMMOH9IV93_BOMMOH9JMY9_BOMMOH9J9P2_BOMMOH9JN76_BOMMOH9JTC5_BOMMOH9IVS9_BOMMOH9IZI1_BOMMOH9IVT6_BOMMOH9JUB6_BOMMOH9JFR3_BOMMOVIT_BOMMOH9JHA7_BOMMOQ2F5Q6_BOMMOH9IZL9_BOMMOH9JYA0_BOMMOH9JRS9_BOMMOH9JBL0_BOMMOH9J011_BOMMOH9JH31_BOMMOSSP2_BOMMOH9JGX1_BOMMOH9JU99_BOMMOH9IZ88_BOMMOH9JAH3_BOMMOH9IX15_BOMMOSI25_BOMMOQ6T3A7_BOMMOH9J585_BOMMOH9JYF4_BOMMOQ9XXZ4_BOMMOH9JK23_BOMMOO01953_BOMMOC7EPE2_BOMMOH9JQH2_BOMMOH9J4L6_BOMMOH9J303_BOMMOH9J453_BOMMOH9J4K5_BOMMOH9JRT0_BOMMOH9J0R5_BOMMOB9VJ79_BOMMOH9J5L5_BOMMOH9IWF3_BOMMOH9J3H2_BOMMOH9IYU4_BOMMOH9JK97_BOMMOL301_BOMMOH9J8B3_BOMMOH9J8I8_BOMMOH9IWI8_BOMMOH9J4L7_BOMMOH9JWN7_BOMMOH9JIB1_BOMMOH9JHM9_BOMMOH9IYF4_BOMMOH9J2F1_BOMMOH9JUB7_BOMMOTCTP_BOMMOH9J5S9_BOMMOH9JPG9_BOMMOH9J593_BOMMOIDGFL_BOMMOH9IZI5_BOMMOH9JL76_BOMMOH9ISJ8_BOMMOH9JA73_BOMMOH9JWW6_BOMMOQ1HPY5_BOMMOBGBP_BOMMOH9J5S6_BOMMOH9JP90_BOMMOH9ISI0_BOMMOH9J243_BOMMOH9IUA7_BOMMOH9J1X1_BOMMOH9ITL0_BOMMOH9J868_BOMMOH9JX84_BOMMOH9JDF0_BOMMOCALR_BOMMOH9JHS4_BOMMOH9JIA9_BOMMOH9JDX3_BOMMOB0ZT34_BOMMOPRP2_BOMMOH9J850_BOMMOH9JQ96_BOMMOQ1EPM0_BOMMOH9IWH9_BOMMOH9JQN8_BOMMOH9JTT6_BOMMOH9JPS6_BOMMOQ1HPY3_BOMMOH9JY09_BOMMOH9JBZ7_BOMMOH9IVR7_BOMMOH9J8I6_BOMMOH9JXK3_BOMMOH9JJV0_BOMMOH9JUB8_BOMMOH9J6I9_BOMMOH9JCK9_BOMMOQ9BPS3_BOMMOH9JUK2_BOMMOH9J8J0_BOMMOH9JIY7_BOMMOH9JKT2_BOMMOH9J8I5_BOMMOH9J3A7_BOMMOH9JGT9_BOMMOH9JLM2_BOMMOH9J9T8_BOMMOH9J1D9_BOMMOQ2F644_BOMMOQ402D9_BOMMOH9JYA3_BOMMOH9JXF8_BOMMOH9J4G1_BOMMOH9J9W8_BOMMOH9JXD8_BOMMOH9J730_BOMMOH9JBC0_BOMMOH9IWJ7_BOMMOH9JEA5_BOMMOH9JD77_BOMMOH9JDQ2_BOMMOH9JN73_BOMMOH9JAS8_BOMMOP27K_BOMMOJHBP_BOMMOLP1_BOMMOH9JNF6_BOMMOA1AT_BOMMOH9IVN9_BOMMOH9JHU5_BOMMOH9J5D7_BOMMOH9JXY6_BOMMOH9J894_BOMMOH9JK41_BOMMOH9IWX2_BOMMOC0H6R2_BOMMOH9IZK4_BOMMOH9JKL1_BOMMOH9JVX1_BOMMOH9JP22_BOMMOH9J4M7_BOMMOH9J9Q8_BOMMOFIBL_BOMMOH9JK39_BOMMOH9JQ40_BOMMOSODC_BOMMOH9JFH1_BOMMOH9J7X3_BOMMOH9J709_BOMMOH9ITR7_BOMMOH9JFA8_BOMMOH9IVS7_BOMMOQ69FX2_BOMMOH9IWH6_BOMMOH9JN98_BOMMOH9JBW7_BOMMOH9JWD5_BOMMOH9IZI4_BOMMOH9JTZ5_BOMMOH9J250_BOMMOH9IU44_BOMMOSGF1_BOMMOH9JBZ4_BOMMOACH1_BOMMOH9J9I7_BOMMOH9J7K1_BOMMOH9J7R4_BOMMOH9JW43_BOMMOH9J1X0_BOMMOH9J1D5_BOMMOE9JEH5_BOMMOH9ISA2_BOMMOPYM_BOMMOH9JT78_BOMMOH9IZ19_BOMMOH9J8H0_BOMMOH9JLC2_BOMMOH9JSY6_BOMMOH9JPE5_BOMMOH9JMS7_BOMMOH9JYA2_BOMMOLP2_BOMMOH9JCC5_BOMMOH9JCP0_BOMMOH9IVS0_BOMMOH9IX10_BOMMOH9JH50_BOMMOH9J5L9_BOMMOQ1HPY8_BOMMOQ6T9Z7_BOMMOFIBH_BOMMOH9JGY3_BOMMOH9ISA5_BOMMOQ5R1P5_BOMMOSSP1_BOMMOH9JK98_BOMMOH9JR42_BOMMOH9ISR3_BOMMOE5EVW2_BOMMOH9J012_BOMMOH9IYR4_BOMMOH9JR22_BOMMOH9J9P6_BOMMOQ2PQU4_BOMMOG8GBC4_BOMMOQ6Q2D6_BOMMOH9JVK2_BOMMOH9J168_BOMMOH9JQU5_BOMMOQ3LB95_BOMMOH9JHU4_BOMMOH9JCD8_BOMMOH9J885_BOMMOH9JXB3_BOMMOH9JTY2_BOMMOH9JAZ9_BOMMOH9JDG1_BOMMOH9J5D8_BOMMOH9JMQ8_BOMMOH9JMY8_BOMMOH9JYJ8_BOMMOH9JHU3_BOMMOH9JXQ6_BOMMOQ2F605_BOMMOH9JDV4_BOMMOH9IS38_BOMMOH9J1A5_BOMMOH9JX51_BOMMOH9JC27_BOMMOH9JB50_BOMMOEF2_BOMMOH9JU96_BOMMOH9J6U8_BOMMOH9B457_BOMMOH9J502_BOMMOH9J4G2_BOMMOB0FPE7_BOMMOH9JI11_BOMMOH9J4V7_BOMMO