A new approach of using modified silver nanoparticles (AgNPs) in toluene as hydrophobic affinity probes for the separation and preconcentration of peptides and proteins in biological samples prior to atmospheric pressure-matrix assisted laser desorption/ionization (AP-MALDI) ion trap mass spectrometry and matrix assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry has been successfully demonstrated. To our best knowledge, for the first time, the modified AgNPs with hydrophobic ligands, such as dodecanethiol (DT) and octadecanethiol (OT) in toluene, were used for the liquid-liquid microextraction (LLME) of peptides and proteins through the hydrophobic interactions. In the present investigation, gramicidin was chosen as a model compound to assess the hydrophobic extraction with the modified AgNPs. The optimum extraction efficiency of gramicidine was observed at pH 7.0 for 1.5 h of extraction time with 7% addition of salt. Compared to the conventional use of AP-MALDI-MS, a 266-388-fold improvement in the limit of detection (LOD) for gramicidin was obtained in urine and plasma samples. The lowest concentration of gramicidin that was detected by using modified AgNPs in urine and plasma samples was 0.13 and 0.16 microM, respectively. Furthermore, the proposed method was demonstrated for the extraction of other long chain proteins, like myoglobin, ubiquitin, and bovine serum albumin, in a sample solution by matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The major feature of the newly synthesized modified AgNPs was that the target species could be efficiently separated and preconcentrated without sample loss prior to MALDI-MS detection for the sensitive and effective analysis of peptides and proteins in biological samples.