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

Coupling a droplet generator with conventional ESI-MS for quantitative analysis of small-volume samples

Quantitative mass spectrometric analysis of small-volume samples (e.g., < 1 μL) has been a challenge mainly due to the difficulties with sample handling and its injection into the system for analysis. Herein we report a microfluidic analytical platform coupling a droplet generator with conventional electrospray ionization-mass spectrometry (ESI-MS) that enables multiple analyses of a μL-sized sample with sensitivity and repeatability. In an analysis by droplet generator-assisted ESI-MS (DG-ESI-MS), a sample of μL volume is pulled into a sampling capillary and its equal nL-sized portions are generated by a droplet generator and analyzed by ESI-MS at time intervals of choice. The droplet generator is made of PMMA sheets by laser engraving conveniently and at a low cost. In a study to achieve effective ESI-MS detection of water-in-oil droplets, it's found that the problem of MS signal suppression by oil can be solved by using an appropriate organic carrier with ESI-enhancing additives. The proposed DG-ESI-MS method has linear calibration curves for both adenine and phenylalanine with LODs at the sub-μM level. Application of the present analytical platform for monitoring substrate concentration changes in an enzymatic reaction solution of 3 μL is demonstrated.

Targeted realignment of LC-MS profiles by neighbor-wise compound-specific graphical time warping with misalignment detection

MOTIVATION

Liquid chromatography-mass spectrometry (LC-MS) is a standard method for proteomics and metabolomics analysis of biological samples. Unfortunately, it suffers from various changes in the retention times (RT) of the same compound in different samples, and these must be subsequently corrected (aligned) during data processing. Classic alignment methods such as in the popular XCMS package often assume a single time-warping function for each sample. Thus, the potentially varying RT drift for compounds with different masses in a sample is neglected in these methods. Moreover, the systematic change in RT drift across run order is often not considered by alignment algorithms. Therefore, these methods cannot effectively correct all misalignments. For a large-scale experiment involving many samples, the existence of misalignment becomes inevitable and concerning.

RESULTS

Here, we describe an integrated reference-free profile alignment method, neighbor-wise compound-specific Graphical Time Warping (ncGTW), that can detect misaligned features and align profiles by leveraging expected RT drift structures and compound-specific warping functions. Specifically, ncGTW uses individualized warping functions for different compounds and assigns constraint edges on warping functions of neighboring samples. Validated with both realistic synthetic data and internal quality control samples, ncGTW applied to two large-scale metabolomics LC-MS datasets identifies many misaligned features and successfully realigns them. These features would otherwise be discarded or uncorrected using existing methods. The ncGTW software tool is developed currently as a plug-in to detect and realign misaligned features present in standard XCMS output.

AVAILABILITY AND IMPLEMENTATION

An R package of ncGTW is freely available at Bioconductor and https://github.com/ChiungTingWu/ncGTW. A detailed user's manual and a vignette are provided within the package.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Correlation of Venom Toxinome Composition of Indian Red Scorpion (Mesobuthus tamulus) with Clinical Manifestations of Scorpion Stings: Failure of Commercial Antivenom to Immune-Recognize the Abundance of Low Molecular Mass Toxins of This Venom

The Indian red scorpion (Mesobuthus tamulus), with its life-threatening sting, is the world's most dangerous species of scorpion. The toxinome composition of M. tamulus venom was determined by tandem mass spectrometry (MS) analysis of venom protein bands separated by SDS-PAGE. A total of 110 venom toxins were identified from searching the MS data against the Buthidae family (taxid: 6855) of toxin entries in nonredundant protein databases. The Na⁺ and K⁺ ion channel toxins taken together are the most abundant toxins (76.7%) giving rise to the neurotoxic nature of this venom. The other minor toxin classes in the M. tamulus venom proteome are serine protease-like protein (2.9%), serine protease inhibitor (2.2%), antimicrobial peptide (2.3%), hyaluronidase (2.2%), makatoxin (2.1%), lipolysis potentiating peptides (1.2%), neurotoxin affecting Cl^- channel (1%), parabutoporin (0.6%), Ca²⁺ channel toxins (0.8%), bradykinin potentiating peptides (0.2%), HMG CoA reductase inhibitor (0.1%), and other toxins with unknown pharmacological activity (7.7%). Several of these toxins have been shown to be promising drug candidates. M. tamulus venom does not show enzymatic activity (phospholipase A₂, l-amino acid oxidase, adenosine tri-, di-, and monophosphatase, hyaluronidase, metalloproteinase, and fibrinogenolytic), in vitro hemolytic activity, interference with blood coagulation, or platelet modulation properties. The clinical manifestations post M. tamulus sting have been described in the literature and are well correlated with its venom proteome composition. An abundance of low molecular mass toxins (3-15 kDa) are responsible for exerting the major pharmacological effects of M. tamulus venom, though they are poorly immune-recognized by commercial scorpion antivenom. This is a major concern for the development of effective antivenom therapy against scorpion stings.

An interstitial peptide is readily processed from within seed proteins

The importance of de novo protein evolution is apparent, but most examples are de novo coding transcripts evolving from silent or non-coding DNA. The peptide macrocycle SunFlower Trypsin Inhibitor 1 (SFTI-1) evolved over 45 million years from genetic expansion within the N-terminal 'discarded' region of an ancestral seed albumin precursor. SFTI-1 and its adjacent albumin are both processed into separate, mature forms by asparaginyl endopeptidase (AEP). Here to determine whether the evolution of SFTI-1 in a latent region of its precursor was critical, we used a transgene approach in A. thaliana analysed by peptide mass spectrometry and RT-qPCR. SFTI could emerge from alternative locations within preproalbumin as well as emerge with precision from unrelated seed proteins via AEP-processing. SFTI production was possible with the adjacent albumin, but peptide levels dropped greatly without the albumin. The ability for SFTI to be processed from multiple sequence contexts and different proteins suggests that to make peptide, it was not crucial for the genetic expansion that gave rise to SFTI and its family to be within a latent protein region. Interstitial peptides, evolving like SFTI within existing proteins, might be more widespread and as a mechanism, SFTI exemplifies a stable, new, functional peptide that did not need a new gene to evolve de novo.

Quantitative MALDI-MS Binding Assays: An Alternative to Radiolabeling

Radiolabeling of ligands is still the gold standard in the study of high-affinity receptor-ligand interactions. In an effort toward safer and simpler alternatives to the use of radioisotopes, we developed a quantitative and highly sensitive matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) method that relies on the use of chemically tagged ligands designed to be specifically detectable when present as traces in complex biological mixtures such as cellular lysates. This innovative technology allows easy, sensitive detection and accurate quantification of analytes at the sub-nanomolar level. After statistical validation, we were able to perform pharmacological evaluations of G protein-coupled receptor (V1A-R)-ligand interactions. Both saturation and competitive binding assays were successfully processed.

Analytical platforms in vitreoretinal proteomics

Current proteomic technologies can effectively be used to study the proteins of the vitreous body and retina in health and disease. The use of appropriate samples, analytical platform and bioinformatic method are essential factors to consider when undertaking such studies. Certain proteins may hinder the detection and evaluation of more relevant proteins associated with pathological processes if not carefully considered, particularly in the sample preparation and data analysis stages. The utilization of more than one quantification technique and database search program to expand the level of proteome coverage and analysis will help to generate more robust and worthwhile results. This review discusses important aspects of sample processing and the use of label and label-free quantitative proteomics strategies applied to the vitreous and retina.

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

The relative quantification and identification of proteins by matrix-assisted laser desorption ionization time-of-flight MS is very important in /MS is very important in protein research and is usually conducted separately. Chemical N-terminal derivatization with 4-sulphophenyl isothiocyanate facilitates de novo sequencing analysis and accurate protein identification, while (18)O labeling is simple, specific and widely applicable among the isotopic labeling methods used for relative quantification. In the present study, a method combining 4-sulphophenyl isothiocyanate derivatization with (18)O isotopic labeling was established to identify and quantify proteins simultaneously in one experiment. Reaction conditions were first optimized using a standard peptide (fibrin peptide) and tryptic peptides from the model protein (bovine serum albumin). Under the optimized conditions, these two independent labeling steps show good compatibility, and the linear relativity of quantification within the ten times dynamic range was stable as revealed by correlation coefficient analysis (R(2) value = 0.998); moreover, precursor peaks in MS/MS spectrum could provide accurate quantitative information, which is usually acquired from MS spectrum, enabling protein identification and quantification in a single MS/MS spectrum. Next, this method was applied to native peptides isolated from spider venoms. As expected, the de novo sequencing results of each peptide matched with the known sequence precisely, and the measured quantitative ratio of each peptide corresponded well with the theoretical ratio. Finally, complex protein mixtures of spider venoms from male and female species with unknown genome information were analyzed. Differentially expressed proteins were successfully identified, and their quantitative information was also accessed. Taken together, this protein identification and quantification method is simple, reliable and efficient, which has a good potential in the exploration of peptides/proteins from species with unknown genome.

Recent methodological advances in MALDI mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is widely used for characterization of large, thermally labile biomolecules. Advantages of this analytical technique are high sensitivity, robustness, high-throughput capacity, and applicability to a wide range of compound classes. For some years, MALDI-MS has also been increasingly used for mass spectrometric imaging as well as in other areas of clinical research. Recently, several new concepts have been presented that have the potential to further advance the performance characteristics of MALDI. Among these innovations are novel matrices with low proton affinities for particularly efficient protonation of analyte molecules, use of wavelength-tunable lasers to achieve optimum excitation conditions, and use of liquid matrices for improved quantification. Instrumental modifications have also made possible MALDI-MS imaging with cellular resolution as well as an efficient generation of multiply charged MALDI ions by use of heated vacuum interfaces. This article reviews these recent innovations and gives the author's personal outlook of possible future developments.