The nanoelectrospray ion source (NanoES) developed recently has proven to be an excellent tool for the sequencing of peptides out of unseparated mixtures. At lower levels of analyte, however, it is increasingly difficult to distinguish the peptide ions in the spectrum, limiting the overall sensitivity of the procedure. Scans for the parents of common fragmentation products of peptides such as immonium ions allow determination of peptide ion masses even when these ions have signal-to-noise ratios of < 1 in the mass spectrum. With this technique, concentration limits for sequencing peptides could be improved to < 5 fmol/microL in favorable cases. Parent ions scan were used to identify posttranslational modifications of peptides in mixtures, with phosphorylation and glycosylation as examples. Detecting phosphorylation by parent scans increased sensitivity by 1-2 orders of magnitude. Modified peptides can be subjected to tandem mass spectrometry in the same experiment to localize the modification. The present approach expands the range of application of nanoelectrospray and complements established liquid chromatography/mass spectrometry methods.