Label-free quantification using MALDI mass spectrometry: considerations and perspectives

Abstract

Profound knowledge of protein abundances in healthy tissues and their changes in disease is crucial for understanding biological processes in basic science and for the development of novel diagnostics and therapeutics. Mass spectrometrybased label-free protein quantification is used increasingly often to gain insights into physiological changes observed in perturbed systems. Although the soft ionization techniques electrospray ionization and matrix-assisted laser desorption/ionization have both been used for protein quantification, this article focuses on instrumental setups with a MALDI ion source. Beside reviewing current bioinformatic data-processing tools for label-free quantification and elaborating on the technical benefits of combining UHPLC and MALDI-MS, we outline the potential of state-of-the-art instruments by reporting unpublished results obtained from twenty-four complex biological samples. This review points out that the capabilities of LC-MALDI MS systems have not yet been fully utilized because of a lack of suitable software tools.

Proteomic tools for environmental microbiology—A roadmap from sample preparation to protein identification and quantification

“…Recent advancements of laser technology allow high‐speed MS/MS data acquisition (up to 2 kHz) and coupling to high‐performance digitizers enables fast analysis of complex samples within a few hours or overnight . In addition, application of LC‐MALDI is increasingly relevant for gel‐free label‐dependent as well as label‐free protein quantification .…”

A Short Overview of the Components in Mass Spectrometry Instrumentation for Proteomics Analyses

“…MALDI works with wide dynamic ranges [29], such as 2 kDa up to 7 kDa, or more [30]. The dominance of singly charged ions, specially for proteins or peptides with molecular weighs 20 kDa is a characteristic of MALDI, in contrast with ESI which produces much more species in higher charges states [31].…”

A method combining SPITC and 18O labeling for simultaneous protein identification and relative quantification

“…With the development of ‘soft’ ionization methods, including electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI), mass spectrometry (MS) provides a particularly sensitive and high‐throughput analytical platform for the efficient identification and quantification of expressed proteins …”

“…With the development of 'soft' ionization methods, including electrospray ionization (ESI) and matrix-assisted laser desorption/ ionization (MALDI), mass spectrometry (MS) provides a particularly sensitive and high-throughput analytical platform for the efficient identification and quantification of expressed proteins. [1][2][3] The numbers of fully-sequenced genomes are increasing rapidly. [4] However, protein identification by MS without sequence information is difficult, because the probability of unambiguous peptide identification is significantly lower than expected.…”