Improved Peptide Recovery in Low-Input MS-Based Proteomics Using High-Recovery StageTip Desalting and Nonionic...

Low-input mass spectrometry (MS)-based proteomics is vulnerable to peptide loss during final sample preparation. We evaluated whether ChocoTip desalting and decyl maltose neopentyl glycol (DMNG)-assisted reconstitution improve peptide recovery from HeLa digests corresponding to 10 ng of protein (∼50 cells). ChocoTip reduces irreversible peptide adsorption into mesopores of chromatographic particles during microscale desalting, whereas DMNG is expected to suppress hydrophobic-interaction-mediated nonspecific adsorption to plasticware during redissolution, transfer, and injection. After selecting DMNG as the nonionic detergent additive, we compared conventional StageTip desalting, ChocoTip desalting, DMNG-assisted reconstitution, and their combination. ChocoTip and DMNG method each improved peptide recovery but affected the peptide populations eluting in different regions of the nanoflow reversed-phase liquid chromatography (nanoRPLC) gradient. Their combination yielded the highest number of peptide identifications and increased peptide intensities across almost the entire nanoRPLC gradient, including commonly identified peptides. Peptides uniquely recovered by the combined workflow covered a broad hydrophobicity range and included longer sequences. These results indicate that suppressing peptide loss at both desalting and post-desalting stages provides a simple strategy to improve sensitivity and peptide coverage in low-input MS-based proteomics.