Serine-threonine kinases and transcription factors play important roles in the G1-S phase progression of the cell cycle. Assays that use quantitative fluorescence by immunocytochemical means, or that measure band strength during Western blot analysis, may have confused interpretations if the intention is to measure G1-S phase commitment of a small subpopulation of phosphorylated proteins, when a larger conversion of the same population of proteins can occur during late G2 and M phases. In mouse trophoblast stem cells (TSC), a human placental cell line (HTR), and/or mouse preimplantation embryos, 8/19 serine-threonine and tyrosine kinases, 3/8 transcription factors, and 8/14 phospho substrate and miscellaneous proteins were phosphorylated at higher levels in M phase than in interphase. Most phosphoproteins appeared to associate with the spindle complex during M phase, but one (p38MAPK) associated with the spindle pole and five (Cdx2, MEK1, 2, p27, and RSK1) associated with the DNA. Phosphorylation was detected throughout apparent metaphase, anaphase and telophase for some proteins, or for only one of these segments for others. The phosphorylation was from 2.1- to 6.2-fold higher during M phase compared with interphase. These data suggest that, when planning and interpreting quantitative data and perturbation experiments, consideration must be given to the role of serine-threonine kinases and transcription factors during decision making in M phase as well as in G1-S phase.