Advances in stem cell proteomics Nade Abazova 1,2,3 and Jeroen Krijgsveld 1,2 Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity. Addresses 1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany 3 European Molecular Biology Laboratory (EMBL), Heidelberg, Germany Corresponding author: Krijgsveld, Jeroen (j.krijgsveld@dkfz.de) Current Opinion in Genetics & Development 2017, 46:149–155 This review comes from a themed issue on Cell reprogramming Edited by Jianlong Wang and Miguel Esteban http://dx.doi.org/10.1016/j.gde.2017.07.007 0959-437X/ã 2017 Elsevier Ltd. All rights reserved. Introduction Stem cell biology is currently one of the most dynamic fields in life science. This is explained by the fact that stem cells are at the basis of organismal development, where intricate mechanisms underlying pluripotency maintenance and cellular specialization are core compo- nents of biological complexity emergence [1]. Addition- ally, the high developmental potential of stem cells and the manifold properties they share with cancer cells hold great promise for a wide range of clinical applications, including drug screens, regenerative medicine and cancer research [2,3]. The vast complexity of stem cell biology demands multi- scale, multi-disciplinary research efforts, including geno- mic, epigenetic and functional studies. Proteomics is making an increasing impact in the field, focusing on proteins as the main functional entities driving cellular processes. This has benefited from technical advances in mass spectrometry for protein identification and quantifi- cation (Box 1) as well as from innovative biochemical approaches to target specific sub-proteomes. Combined with tailor-made bioinformatic tools, this now provides an integrated and accessible set of technologies to charac- terize cellular proteomes at unprecedented depth and detail. Here we review recent advances in stem cell proteomics, highlighting how quantitative studies of pro- tein expression, localization, interaction and modification have contributed to increase our understanding of stem cell identity, cell fate transitions, and chromatin regula- tion (Figure 1). Proteomic profiling of cellular plasticity Proteomics of stem cells in vitro Mass-spectrometry-based proteomics has been applied to a wide range of developmental processes including sper- matogenesis [4], lineage specification [5] and neural dif- ferentiation [6], among many others in a body of literature that exceeds the scope of this review. Clearly the number and diversity of proteomic applications in the stem cell field are the result of continuous progress in introducing various in vitro cell culture systems that recapitulate specific developmental processes that are not easily acces- sible in vivo. A prominent example is the introduction of iPS cells to study fundamental aspects of gain and loss of pluripotency, in which proteomics is taking an increasing share [7]. For instance, the groups of Nagy and Heck identified two waves in proteome resetting in the early and late phase of reprogramming of secondary mouse embryonic fibroblasts (MEFs) to iPS cells [8], mirroring findings from our lab in a similar system [9]. The prote- ome data covered extensive cellular programs such as energy metabolism, chromatin regulation and cell cycle, reflecting a profound but well-orchestrated transition in cell identity. Other studies have focused on characteriz- ing the molecular basis of pluripotency by comparing proteomes of mouse embryonic stem cells (mESCs) in ground state and primed state (epiblast stem cells, EpiSC) of pluripotency, identifying global differences in glycolysis [10] and in many proteins involved in chro- matin regulation [10,11], reflecting the notion that plur- ipotency is largely regulated epigenetically [12]. Proteomics of stem cells in vivo Although in vitro systems are very powerful to create (generally) homogeneous populations under well-con- trolled conditions, the ultimate goal is to understand cellular plasticity in the complex environment of the stem cell niche in vivo. Challenged by the low number of cells that can typically be obtained from animal models, Available online at www.sciencedirect.com ScienceDirect www.sciencedirect.com Current Opinion in Genetics & Development 2017, 46:149–155