Accurate mass values as obtainable by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) were employed in a theoretical study to differentiate between nonmodified and phosphorylated peptides. It was found that for peptide masses up to 1000 u more than 98% of all theoretical monophosphorylated peptides (all possible combinations of proteinogenic amino acids having one phosphorylation on S, T, or Y) can be distinguished from nonphosphorylated peptides directly by their mass, if mass values are determined with an accuracy of better than Ϯ0.1 ppm. At a peptide mass of 1500 u still 70% of all possible monophosphorylated peptides are distinguishable from nonmodified peptides by their accurate mass alone. In contrast to established techniques of data-dependent multidimensional mass spectrometry, only the mass of the precursor ion is necessary to decide upon subsequent fragment ion analysis of a peptide for sequence analysis in an LC-MS/MS investigation of a complex sample, when using a precalculated mass distribution A ccurate masses of molecules or molecular ions build up a discrete structure in mass space, as a result of the mass defect of the isotopes they are composed of. Masses of atoms are therefore not the sum of masses of a certain number of nuclear protons and neutrons plus the sum of masses of electrons, but include an additional mass deficit due to the specific nuclear binding energies of the atom. As a result, each isotopic species carries a characteristic mass signature expressed as an isotope-specific accurate mass value and furthermore, each molecule carries digital signatures (i.e., number and accurate mass) of their atomic building blocks. Regarding the mass space of different substance classes such as peptides, carbohydrates, or lipids, varying ratios of their common elements (CHNOS) lead to accurate-mass distributions, which do not necessarily overlap and therefore can eventually be used for substance class identification (Figure 1a). If elemental compositions of different substance class molecules are identical accidentally, however, accurate masses are identical and cannot be resolved even with the highest mass resolving power.When introducing a new element, on the other hand, accurate mass distributions definitely become distinguishable, since the mass defect of the added element results in a new signature of the accurate masses of the molecules. This is the case, for example, when comparing nonmodified and phosphorylated peptides. With a sufficiently high mass resolving power, such species can always be distinguished from each other. As instruments for determining molecular masses are getting more and more accurate with higher and higher mass resolution, investigation of this structure is becoming an important and fundamental scientific goal. Today, mass accuracies in the range of Ϯ0.2 ppm can routinely be achieved with internal calibration on ion trap Fourier transform ion cyclotron resonance mass spectrometers [1][2][3][4], and it is quite likely that the Ϯ0.1 ppm range of m...