Continuous sample deposition from reversed-phase liquid chromatography to tracks on a matrix-assisted laser desorption/ionization precoated target for the analysis of protein digests

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Abstract
Peptide mass fingerprinting by matrix‐assisted laser desorption/ionization (MALDI)‐mass spectrometry (MS) is one of the standard high‐throughput methods for protein identification today. Traditionally this method has been based on spotting peptide mixtures onto MALDI targets. While this method works well for more abundant proteins, low‐abundance proteins mixed with high‐abundance proteins tend to go undetected due to ion suppression effects, instrumental dynamic range limitations and chemical noise interference. We present an alternative approach where liquid chromatography (LC) effluent is continuously collected as linear tracks on a MALDI target. In this manner the chromatographic separation is spatially preserved on the target, which enables generation of off‐line LC‐MS and LC‐MS/MS data by MALDI. LC‐MALDI sample collection provides improved sensitivity and dynamic range, spatial resolution of peptides along the sample track, and permits peptide mass mapping of low‐abundance proteins in mixtures containing high‐abundance proteins. In this work, standard and ribosomal protein digests are resolved and captured using LC‐MALDI sample collection and analyzed by MALDI‐TOF‐MS.