The native subcellular location (also referred to as localization or cellular compartment) of a protein is the one in which it acts most frequently; it is one aspect of protein function. Do ten eukaryotic model organisms differ in their location spectrum, i.e., the fraction of its proteome in each of seven major cellular compartments? As experimental annotations of locations remain biased and incomplete, we need prediction methods to answer this question. After systematic bias corrections, the complete but faulty prediction methods appeared to be more appropriate to compare location spectra between species than the incomplete more accurate experimental data. This work compared the location spectra for ten eukaryotes: Homo sapiens (human), Gorilla gorilla (gorilla), Pan troglodytes (chimpanzee), Mus musculus (mouse), Rattus norvegicus (rat), Drosophila melanogaster (fruit/vinegar fly), Anopheles gambiae (African malaria mosquito), Caenorhabitis elegans (nematode), Saccharomyces cerevisiae (baker’s yeast), and Schizosaccharomyces pombe (fission yeast). The two largest classes were predicted to be the nucleus and the cytoplasm together accounting for 47–62% of all proteins, while 7–21% of the proteins were predicted in the plasma membrane and 4–15% to be secreted. Overall, the predicted location spectra were largely similar. However, in detail, the differences sufficed to plot trees (UPGMA) and 2D (PCA) maps relating the ten organisms using a simple Euclidean distance in seven states (location classes). The relations based on the simple predicted location spectra captured aspects of cross-species comparisons usually revealed only by much more detailed evolutionary comparisons. Most interestingly, known phylogenetic relations were reproduced better by paralog-only than by ortholog-only trees.

蛋白质的天然亚细胞位置（也称为定位或细胞区室）是其作用最频繁的位置。这是蛋白质功能的一个方面。十种真核模式生物的定位谱是否不同，即其蛋白质组在七个主要细胞区室中的每一个中的比例？由于位置的实验注释仍然存在偏差和不完整，我们需要预测方法来回答这个问题。在系统偏差校正之后，完整但错误的预测方法似乎比不完整的更准确的实验数据更适合比较物种之间的位置光谱。这项工作比较了十种真核生物的位置光谱：Homo sapiens（人类）、Gorilla gorilla（大猩猩）、Pan troglodytes（黑猩猩）、Mus musculus（小鼠）、Rattus norvegicus（大鼠）、Drosophila melanogaster（水果/醋蝇）、Anopheles gambiae（非洲疟疾蚊子）、Caenorhabitis elegans（线虫）、Saccharomyces cerevisiae（面包酵母） ) 和粟酒裂殖酵母（裂变酵母）。预计最大的两个类别是细胞核和细胞质，共占所有蛋白质的 47-62%，而质膜中预测的蛋白质占 7-21%，分泌的蛋白质占 4-15%。总体而言，预测的位置光谱非常相似。然而，详细地说，这些差异足以绘制树 (UPGMA) 和 2D (PCA) 地图，使用简单的欧几里德距离在七个状态（位置类）中关联十种生物。基于简单预测位置谱的关系捕获了跨物种比较的各个方面，通常只能通过更详细的进化比较来揭示。最有趣的是，已知的系统发育关系通过仅旁系同源树比仅由直系同源树复制得更好。