1. A method for exploration, production, and development of hydrocarbons comprising: obtaining a sample comprising hydrocarbons; analyzing the sample for a geochemical signature, wherein the geochemical signature comprises one or more of a multiply substituted isotopologue signature and a position specific isotope signature; determining one or more of type of alteration and extent of alteration, wherein the determining comprises comparing one or more of the multiply substituted isotopologue signature and position specific isotope signature of isotopes of different species of hydrocarbon compounds; and developing or refining an exploration, development, or production strategy based on the determined one or more of one of type of alteration and extent of alteration.