代谢物组（英语：Metabolome）是指在一个生物样品中发现的完整的一套小分子化学物质。所述生物样品可以是一个细胞，一个细胞器，一个器官，一个组织，一个组织提取物，一个生物流体或整个生物体。在给定的代谢物组发现的小分子的化学物质可能既包括内源性代谢物，它们是由生物体天然产生的（如氨基酸，有机酸，核酸，脂肪酸，胺，糖，维生素，辅因子，颜料，抗生素等），又包括外源化学物质（如药物，环境污染物，食品添加剂，毒素和其它生物异源物质），它们不是由生物体天然产生的。换句话说，代谢物组既有内源性代谢物组又有外源性代谢物组。内源性代谢物组可进一步细分为包括“初级”的和“次级”的代谢物组（特别是指植物的或微生物的代谢物组时）。初级代谢产物是直接参与正常的生长，发育和繁殖。次级代谢产物并不直接参与这些过程，但通常具有重要的生态功能。次级代谢产物可能包括色素，抗生素或部分生物异源物质代谢废物的衍生产品。一个小分子有资格作为一种代谢物，或者被认为是代谢物组的一部分，必须通常具有分子量<1500道尔顿。这意味着例如糖脂，多糖，短肽（<14个氨基酸）和小的寡核苷酸（<5个碱基）的分子可以视为代谢物质或代谢物组的成分。另一方面，非常大的高分子，如蛋白质，信使RNA，核糖体RNA，microRNA和脱氧核糖核酸(DNA)绝对不是代谢物质，并且不被认为是代谢物组的一部分。代谢物组的研究被称为代谢物组学。图1所示为不同的“组学”之间的关系的图片。

The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants, food additives, toxins and other xenobiotics) that are not naturally produced by an organism. In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A primary metabolite is directly involved in the normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has important ecological function. Secondary metabolites may include pigments, antibiotics or waste products derived from partially metabolized xenobiotics. To qualify as a metabolite, or to be considered to be part of the metabolome, a small molecule must typically have a molecular weight <1500 Da. This means that molecules such as glycolipids, polysaccharides, short peptides (<14 amino acids) and small oligonucleotides (<5 bases) can be regarded as metabolites or constituents of the metabolome. On the other hand, very large macromolecules such as proteins, messenger RNA, ribosomal RNA, microRNA and DNA are definitely not metabolites and are not considered to be part of the metabolome. The study of the metabolome is called metabolomics. See Figure 1 for a picture of the relationship between different “omes”.