Derivatization by 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate for enhancing the ionization yield of small peptides and glycopeptides in matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry

Enhanced carboxypeptidase efficacies and differentiation of peptide epimers

Carboxypeptidases enzymatically cleaves the peptide bond of C-terminal amino acids within peptides. In humans, it is involved in enzymatic synthesis and maturation of proteins and peptides. Carboxypeptidases A and Y have difficulty hydrolyzing the peptide bond of dipeptides and some other amino acid sequences. Early investigations into different N-blocking groups concluded that larger moieties increased substrate susceptibility to peptide bond hydrolysis with carboxypeptidase. This study conclusively demonstrates that 6-aminoquinoline-N-hydroxysuccimidyl carbamate (AQC) as an N-blocking group greatly enhances substrate hydrolysis with carboxypeptidase. AQC addition to the N-terminus of amino acids and peptides also improves chromatographic peak shape and sensitivities via mass spectrometry detection. These enzymes have been used for amino acid sequence determination prior to the advent of modern proteomics. However, most modern proteomic methods assume that all peptides are comprised of l-amino acids and therefore cannot distinguish L-from d-amino acids within the peptide sequence. The majority of existing methods that allow for chiral differentiation either require synthetic standards or incur racemization in the process. This study highlights the resistance of d-amino acids within peptides to enzymatic hydrolysis by Carboxypeptidase Y. This stereoselectivity may be advantageous when screening low abundance peptide epimers.

High-throughput and high-sensitivity N-Glycan profiling: A platform for biopharmaceutical development and disease biomarker discovery

Protein glycosylation contributes to critical biological function of glycoproteins. Glycan analysis is essential for the production of biopharmaceuticals as well as for the identification of disease biomarkers. However, glycans are highly heterogeneous, which has considerably hampered the progress of glycomics. Here, we present an improved 96-well plate format platform for streamlined glycan profiling that takes advantage of rapid glycoprotein denaturation, deglycosylation, fluorescent derivatization, and on-matrix glycan clean-up. This approach offers high sensitivity with consistent identification and quantification of diverse N-glycans across multiple samples on a high-throughput scale. We demonstrate its capability for N-glycan profiling of glycoproteins from various sources, including two recombinant monoclonal antibodies produced from Chinese Hamster Ovary cells, EG2-hFc and rituximab, polyclonal antibodies purified from human serum, and total glycoproteins from human serum. Combined with the complementary information obtained by sequential digestion from exoglycosidase arrays, this approach allows the detection and identification of multiple N-glycans in these complex biological samples. The reagents, workflow, and Hydrophilic interaction liquid chromatography with fluorescence detection (HILIC-FLD), are simple enough to be implemented into a straightforward user-friendly setup. This improved technology provides a powerful tool in support of rapid advancement of glycan analysis for biopharmaceutical development and biomarker discovery for clinical disease diagnosis.

GlycoHunter: An Open-Source Software for the Detection and Relative Quantification of INLIGHT-Labeled N-Linked Glycans

Glycans are responsible for many biological activities; however, their structures are incredibly diverse and complex, often rendering the field of glycomics unsolvable by a single analytical technique. The development of multiple chemical derivatization strategies and bioinformatic software is responsible for some of the greatest analytical gains in the field of glycomics. The INLIGHT strategy is a chemical derivatization technique using hydrazide chemistry to derivatize the reducing end of N-linked glycans and incorporates either a natural (NAT, ¹²C₆) or a stable-isotope label (SIL, ¹³C₆) to carry out relative quantification. Here we present GlycoHunter, a user-friendly software created in MATLAB that enables researchers to accurately and efficiently process MS1 glycomics data where a NAT and SIL pair is generated for relative quantification, including but not limited to, INLIGHT. GlycoHunter accepts the commonly used data file formats imzML and mzXML and effectively identifies all peak pairs associated with NAT- and SIL-labeled N-linked glycans using MS1 data. It also includes the ability to tailor the search parameters and export the results for further analysis using Skyline or Excel.

Reliable and generic liquid chromatography/mass spectrometry quantification of short peptides using a stable-isotope-labeled labeling agent

RATIONALE

It is important to investigate the behavior of protein hydrolysate components in both in vitro and in vivo studies, to support the elucidation of their biological functions. As protein hydrolysates and biological matrices are highly complex mixtures, it is essential to apply fully reliable and flexible analytical approaches.

METHODS

A novel and generic Liquid Chromatography/Mass Spectrometry methodology was developed to analyze short peptides. A stable-isotope-labeled labeling agent 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (¹³ C₃ ) was synthesized and used to prepare internal standards from non-labeled analyte peptides. The amino acid and peptides p, pG, Pp, GPp and PpG (where p stands for hydroxyproline) were used for proof of principle.

RESULTS

The method showed acceptable performance in solvent, in simulated gastrointestinal fluid and in serum. The (linear) dynamic range expanded to over four orders of magnitude, which is very useful when multiple analytes are analyzed in a biological matrix, due to the large differences in concentrations observed for endogenous and protein hydrolysate components. The method provides absolute-quantitative results and is fully accountable on the single-sample and single-component level.

CONCLUSIONS

The methodology can be applied to reliably quantify protein hydrolysate nutraceutical components at various stages during their in vivo processing. Internal standards can also be synthesized for other short peptides whenever they are expected to have biological relevance and require quantification. Overall this provides an excellent analytical tool to support the elucidation of the biological functions of protein hydrolysate components.

Application of 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate derivatization for enhanced peptide mapping analysis of non-biological complex drug glatiramer acetate using liquid chromatography/electrospray ionization collision-induced dissociation high-resolution mass spectrometry

RATIONALE

Glatiramer acetate (GA) (Copaxone®) is a non-biological complex drug (NBCD) comprising random-sequence polymer chains of four amino acids (MW ~ 5-9 kDa) with unknown structure. The characterization of NBCDs by reversed-phase liquid chromatography/mass spectrometry (RPLC/MS) peptide mapping is often impeded by insufficient separation and/or low sensitivity. To overcome this issue, pre-column derivatization of GA peptide digest was used to improve RPLC/MS detectability and to generate a comprehensive peptide profile.

METHODS

Amino groups of peptides generated by trypsin digestion of GA were derivatized using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) reagent. The derivatized mixture of random-sequence peptides was analyzed by liquid chromatography/positive-mode electrospray ionization collision-induced dissociation high-resolution mass spectrometry (RPLC/ESI-CID-HRMS/MS). Data-independent LC/MS^E mode was used for data acquisition.

RESULTS

The derivatization of the GA peptide mixture increased the detectability of RPLC/ESI-CID-HRMS/MS analysis. The efficacy of the procedure was demonstrated by using selected peptides related to different polymeric chain origins. The resultant peptides were derivatized in a predictable manner giving a minimum of side products. The reproducibility of the developed method was demonstrated by comparing peptide elution profiles derived from six Copaxone® lots.

CONCLUSIONS

Application of the AQC pre-column derivatization provides a framework that could be used as an attractive approach for monitoring the quality and characterization of NBCD products in the pharmaceutical industry.

Non-targeted and targeted analysis of collagen hydrolysates during the course of digestion and absorption

Protein hydrolysates are an important part of the human diet. Often, they are prepared from milk, soy, or collagen. In the present study, four different collagen hydrolysates were tested, varying in the average molecular weight and the animal source. Three types of samples, the dissolved start products, in vitro generated dialysates (containing the digested components that are potentially available for small intestinal absorption), and human serum collected after product ingestion, were analyzed using LC-MS to compare the state of the hydrolysates before and after absorption, i.e., uptake into the blood. It was found that the composition of the collagen hydrolysates prior to and after ingestion was highly complex and dynamic, which made it challenging to predefine a strategy for a targeted analysis. Therefore, we implemented a new analytical approach to first map hydrolysate data sets by performing non-targeted LC-MS analysis followed by non-targeted and targeted data analysis. It was shown that the insight gained by following such a top down (data) analytical workflow could be crucial for defining a suitable targeted setup and considering data trends beyond the defined targets. After having defined and performed a limited targeted analysis, it was found that, in our experimental setup, Hyp-Gly and especially Pro-Hyp contributed significantly as carrier to the total Hyp increase in blood after ingestion of collagen hydrolysate.

Combination of an AccQ•Tag-Ultra-Performance Liquid Chromatographic Method with Tandem Mass Spectrometry for the Analysis of Amino Acids

Amino acid analysis is a powerful tool in life sciences. Current analytical methods used for the detection and quantitation of low abundance amino acids in complex samples face intrinsic challenges such as insufficient sensitivity, selectivity, and throughput. This chapter describes a protocol that makes use of AccQ•Tag chemical derivatization combined with the exceptional chromatographic resolution of ultra-performance liquid chromatography (UPLC) and the sensitivity and selectivity of tandem mass spectrometry (MS/MS). The method has been fully implemented and validated using different tandem quadrupole detectors and thoroughly tested for a variety of samples such as P. falciparum, human red blood cells, and Arabidopsis thaliana extracts. Compared to currently available methods for amino acid analysis, the AccQ•Tag UPLC-MS/MS method presented here provides enhanced sensitivity and reproducibility and offers excellent performance within a short analysis time and a broad dynamic range of analyte concentration. The focus of this chapter is the application of this improved protocol for the compositional amino acid analysis in Arabidopsis thaliana leaf extracts using the Xevo TQ for mass spectrometric detection.

MALDI-TOF mass spectrometry-based quantification of C-peptide in diabetes patients

BACKGROUND

Serum C-peptide concentrations reflect insulin secretion and beta cell function and can be used to diagnose and distinguish type-1 and type-2 diabetes. C-peptide is a more accurate indicator of insulin status than direct insulin measurement for monitoring patients with diabetes. However, the current methods available for C-peptide quantification exhibit poor reproducibility, are costly, and require highly trained laboratory personnel. Here, we have developed and evaluated a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assay to standardize C-peptide measurements, providing highly accurate and comparable results across testing systems and laboratories.

METHODS

C-peptide from human serum was enriched using antibody-conjugated magnetic beads. The eluted isolates were further modified with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) to enhance the ionization of naturally acidic C-peptide. After desalting with ZipTips, the samples were subjected to MALDI-TOF MS analysis. Recombinant human C-peptide was used to develop the assay, and a heavy isotope labeled human C-peptide was used as an internal standard for quantification.

RESULTS

The MALDI-TOF MS method was validated in accordance with the restrictions of the device, with a limit of quantitation of 25 pmol/L. A correlation between the MAL-DI-TOF MS assay and a reference method was conducted using patient samples. The resulting regression revealed good agreement.

CONCLUSIONS

A simple, high-throughput, cost effective and quantitative MALDI-TOF MS C-peptide assay has been successfully developed and validated in clinical serum samples.

The sweet spot for biologics: recent advances in characterization of biotherapeutic glycoproteins

INTRODUCTION

Glycosylation is recognized as a Critical Quality Attribute for therapeutic glycoproteins such as monoclonal antibodies, fusion proteins and therapeutic replacement enzymes. Hence, efficient and quantitative glycan analysis techniques have been increasingly important for their discovery, development and quality control. The aim of this review is to highlight relevant and recent advances in analytical technologies for characterization of biotherapeutic glycoproteins. Areas covered: The review gives an overview of the glycosylation trends of biotherapeutics approved in 2016 and 2017 by FDA. It describes current and novel analytical technologies for characterization of therapeutic glycoproteins and is explored in the context of released glycan, glycopeptide or intact glycoprotein analysis. Ultra performance liquid chromatography, mass spectrometry and capillary electrophoresis technologies are explored in this context. Expert commentary: There is a need for the biopharmaceutical industry to incorporate novel state of the art analytical technologies into existing and new therapeutic glycoprotein workflows for safer and more efficient biotherapeutics and for the improvement of future biotherapeutic design. Additionally, at present, there is no 'gold-standard' approach to address all the regulatory requirements and as such this will involve the use of orthogonal glycoanalytical technologies with a view to gain diagnostic information about the therapeutic glycoprotein.

Ghost peaks observed after atmospheric pressure matrix-assisted laser desorption/ionization experiments may disclose new ionization mechanism of matrix-assisted hypersonic velocity impact ionization

RATIONALE

Understanding the mechanisms of matrix-assisted laser desorption/ionization (MALDI) promises improvements in the sensitivity and specificity of many established applications in the field of mass spectrometry. This paper reports a serendipitous observation of a significant ion yield in a post-ionization experiment conducted after the sample had been removed from a standard atmospheric pressure (AP)-MALDI source. This post-ionization is interpreted in terms of collisions of microparticles moving with a hypersonic velocity into a solid surface. Calculations show that the thermal energy released during such collisions is close to that absorbed by the top matrix layer in traditional MALDI. The microparticles, containing both the matrix and analytes, could be detached from a film produced inside the inlet capillary during the sample ablation and accelerated by the flow rushing through the capillary. These observations contribute some new perspective to ion formation in both laser and laser-less matrix-assisted ionization.

METHODS

An AP-MALDI ion source hyphenated with a three-stage high-pressure ion funnel system was utilized for peptide mass analysis. After the laser had been turned off and the MALDI sample removed, ions were detected during a gradual reduction of the background pressure in the first funnel. The constant-rate pressure reduction led to the reproducible appearance of different singly and doubly charged peptide peaks in mass spectra taken a few seconds after the end of the MALDI analysis of a dried-droplet spot.

RESULTS

The ion yield as well as the mass range of ions observed with a significant delay after a completion of the primary MALDI analysis depended primarily on the background pressure inside the first funnel. The production of ions in this post-ionization step was exclusively observed during the pressure drop. A lower matrix background and significant increase in relative yield of double-protonated ions are reported.

CONCLUSIONS

The observations were partially consistent with a model of the supersonic jet from the inlet capillary accelerating detached particles to kinetic energies suitable for matrix-assisted hypersonic-velocity impact ionization.

A novel method of liquid chromatography-tandem mass spectrometry combined with chemical derivatization for the determination of ribonucleosides in urine

Ribonucleosides are the end products of RNA metabolism. These metabolites, especially the modified ribonucleosides, have been extensively evaluated as cancer-related biomarkers. However, the determination of urinary ribonucleosides is still a challenge due to their low abundance, high polarity and serious matrix interferences in urine samples. In this study, a derivatization method based on a chemical reaction between ribonucleosides and acetone to form acetonides was developed for the determination of urinary ribonucleosides. The derivative products, acetonides, were detected by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methodological evaluation was performed by quantifying four nucleosides for linear range, average recovery, precision, accuracy and stability. The validated procedures were applied to screen modified ribonucleosides in urine samples. Improvement of separation and enhancement of sensitivity were obtained in the analysis. To identify ribonucleosides, inexpensive isotope labeling acetone (acetone-d6) and label-free acetone were applied to form ordinary and deuterated acetonides, respectively. The two groups of samples were separated with orthogonal partial least squares (OPLS). The ordinary and deuterated pairs of acetonides were symmetrically distributed in the S-plot for easy and visual signal identification. After structural confirmation, a total of 56 ribonucleosides were detected, 52 of which were modified ribonucleosides. The application of derivatization, deuterium-labeling and multivariate statistical analysis offers a new option for selective detection of ribonucleosides in biological samples.

Determination of hemocoagulase agkistrodon in a pharmaceutical preparation by high-performance liquid chromatography with pre-column derivatization and fluorescence detection

Currently, there is no analytical method for the quantification of hemocoagulase agkistrodon (HCA) in pharmaceutical preparations. This study presents a pre-column derivatization method for the quantification of HCA, a compound extracted from the venom of Agkistrodon acutus, in a pharmaceutical preparation (trade name Suling). In the proposed method, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate was used to tag the HCA substrate, and the derivatives were analyzed by high-performance liquid chromatography with fluorescence detection. Complete and homogeneous derivatization of HCA was confirmed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry analysis. The specificity of the method was validated by forced degradation, and interference was assessed using a placebo. Under the optimum chromatographic conditions, the calibration curve was linear over a range of 10 to 500 ng/mL, featuring a correlation coefficient of 0.9999. The limits of detection and quantification of the method were 0.57 and 1.6 ng/mL, respectively. The percentage recovery of HCA in quality control samples ranged from 97.49 to 99.15%. Overall, this novel method can be applied to the quantitative determination of HCA in pharmaceutical preparations.

High sensitivity mass spectrometric quantification of serum growth hormone by amphiphilic peptide conjugation

Amphiphilic peptide conjugation affords a significant increase in sensitivity with protein quantification by electrospray-ionization mass spectrometry. This has been demonstrated for human growth hormone (GH) in serum using N-(3-iodopropyl)-N,N,N-dimethyloctylammonium iodide as derivatizing reagent. The signal enhancement achieved is up to a factor of 5-6 and enables extension of the applicable concentration range down to the very low concentrations (≤ 1.0 µg/L) as encountered with clinical glucose suppression tests for patients with acromegaly. The method has been validated using a set of serum samples spiked with known amounts of recombinant 22 kDa GH in the range of 0.48 to 7.65 µg/L. The coefficient of variation (CV) calculated based on the deviation of results from the expected concentrations was 3.5%. The limit of detection (LoD) was determined as 0.1 µg/L and the limit of quantification (LoQ) as 0.4 µg/L. The potential of the method as a tool in clinical practice has been demonstrated with patient samples of about 1 µg/L.

Tunable charge tags for electron-based methods of peptide sequencing: design and applications

Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixed-charge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal c-type fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for N-terminal tagging of Arg-containing tryptic peptides.

Combination of an AccQ·Tag-ultra performance liquid chromatographic method with tandem mass spectrometry for the analysis of amino acids

Amino acid analysis is a powerful tool in life sciences. Current analytical methods used for the detection and quantitation of low abundance amino acids in complex samples face intrinsic challenges such as insufficient sensitivity, selectivity, and throughput. This chapter describes a protocol that makes use of AccQ∙Tag chemical derivatization combined with the exceptional chromatographic resolution of ultra performance liquid chromatography (UPLC), and the sensitivity and selectivity of tandem mass spectrometry (MS/MS). The method has been fully implemented and validated using different tandem quadrupole detectors, and thoroughly tested for a variety of samples such as Plasmodium falciparum, human red blood cells, and Arabidopsis thaliana extracts. Compared to currently available methods for amino acid analysis, the AccQ∙Tag UPLC-MS/MS method presented here provides enhanced sensitivity and reproducibility, and offers excellent performance within a short analysis time and a broad dynamic range of analyte concentration. The focus of this chapter is the application of this improved protocol for the compositional amino acid analysis in A. thaliana leaf extracts using the Xevo TQ for mass spectrometric detection.

Reagent precoated targets for rapid in-tissue derivatization of the anti-tuberculosis drug isoniazid followed by MALDI imaging mass spectrometry

Isoniazid (INH) is an important component of front-line anti-tuberculosis therapy with good serum pharmacokinetics but unknown ability to penetrate tuberculous lesions. However, endogenous background interferences hinder our ability to directly analyze INH in tissues. Chemical derivatization has been successfully used to measure isoniazid directly from tissue samples using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). MALDI targets were pretreated with trans-cinnamaldehyde (CA) prior to mounting tissue slices. Isoniazid present in the tissues was efficiently derivatized and the INH-CA product measured by MS/MS. Precoating of MALDI targets allows the tissues to be directly thaw-mounted and derivatized, thus simplifying the preparation. A time-course series of tissues from tuberculosis infected/INH dosed animals were assayed and the MALDI MS/MS response correlates well with the amount of INH determined to be in the tissues by high-performance liquid chromatography (HPLC)-MS/MS.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006

This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.

Alkylating tryptic peptides to enhance electrospray ionization mass spectrometry analysis

A major limitation of mass spectrometry-based proteomics is inefficient and differential ionization during electrospray ionization (ESI). This leads to problems such as increased limits of detection and incomplete sequence coverage of proteins. Incomplete sequence coverage is especially problematic for analyses that require the detection and identification of specific peptides from a protein, such as the analysis of post-translational modifications. We describe here the development and use of aldehyde-based chemistry for the alkylation of peptide primary amines to increase peptide hydrophobicity, providing increased ionization efficiency and concomitant signal enhancement. When employed to modify the peptide products of protein tryptic digests, increased sequence coverage is obtained from combined modified and unmodified digests. To evaluate the utility of alkylation of peptides for selected reaction monitoring (SRM) assays, we alkylated a peptide from the protein Oct4, known to play a role in regulating stem cell differentiation. Increased chromatographic retention and ionization efficiency is observed for the alkylated Oct4 peptide compared to its unmodified form.

Improving limits of detection for B-type natriuretic peptide using PC-IDMS: an application of the ALiPHAT strategy

Hydrophobic tagging of biomolecules has been reported by our group and others to increase their ionization efficiency during electrospray ionization and facilitate their detection by mass spectrometry. As such, hydrophobic tagging should provide a viable method for augmenting MS-based quantification of low abundance proteins by decreasing their detection limits. Herein we have evaluated two commercial alkylation reagents and several newly synthesized hydrophobic alkylation reagents for their utility in quantifying B-type Natriuretic Peptide, a low abundance cardiac biomarker, by protein cleavage isotope dilution mass spectrometry. For the cysteine containing tryptic peptide evaluated, a approximately 3.5-fold decrease in the detection limit was observed for the best performing hydrophobic reagent, 2-iodo-N-octylacetamide, relative to the commonly used alkylation reagent, iodoacetamide. Additionally, we have evaluated the use of nonpolar surface areas as a metric for assessing the effectiveness of the alkylation reagents in improving ESI response.

Evaluation of the ALiPHAT method for PC-IDMS and correlation of limits-of-detection with nonpolar surface area

PC-IDMS experiments for two peptides, laminin nonapeptide and the N-terminal tryptic peptide of prostate specific antigen, were performed utilizing a variety of alkylating reagents. These experiments were conducted to investigate how hydrophobicity influences the limits-of-detection (LOD) by altering their electrospray ionization response. Nonpolar surface areas were calculated for both peptides and all alkylating reagents to provide an estimate of the hydrophobicity of the differently alkylated peptides. Decreases in LOD by 2-fold were observed for both peptides between the best and worst performing combination of alkylating reagent. However, while an increase in hydrophobicity was found to aid in decreasing LOD to an extent, beyond a certain hydrophobicity, we observed a decrease.

Applications of chemical tagging approaches in combination with 2DE and mass spectrometry

Chemical modification reactions play an important role in various protocols for mass-spectrometry-based proteome analysis; this applies to both gel-based and gel-free proteomics workflows. In combination with two-dimensional gel electrophoresis (2DE), the addition of "tags" by means of chemical reactions serves several purposes. Potential benefits include increased sensitivity or sequence coverage for peptide mass fingerprinting and improved peptide fragmentation for de novo sequencing studies. Tagging strategies can also be used to obtain complementary quantitative information in addition to densitometry, and they may be employed for the study of post-translational modifications. In combination with the unique advantages of 2DE as a separation technique, such approaches provide a powerful toolbox for proteomic research. In this review, relevant examples from recent literature will be given to illustrate the capabilities of chemical tagging approaches, and methodological requirements will be discussed.

Lys Tag: an easy and robust chemical modification for improved de novo sequencing with a matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometer

Mass spectrometry using a matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) instrument is a widespread technique for various types of proteomic analysis. Along with an expanding interest in proteomics, there is a strong requirement for the identification of proteins with high confidence from biological samples. Peptide modification by a wide variety of post-translational modifications (PTMs), the existence of different protein isoforms and the presence of uncharacterized genomes of many species, make protein identification through peptide mass fingerprinting (PMF) often unachievable. Peptide de novo sequencing has been proven to be a useful approach to overcome these variables, and efficient derivatization processes are important tools to achieve this goal. In the present work we describe the methodology and experimental applications of a fast, efficient and cheap lysine derivatization. This chemical modification improves the signals from lysine-terminated peptides and can be efficiently used as a lysine-blocking agent in combination with other derivatization techniques. Most importantly, upon peptide fragmentation it generates a neat series of predominantly y-ions, allowing the determination of unambiguous amino acid sequences. Moreover, this chemical compound was used with target-eluted samples, enabling a second, alternative analysis of the same sample in the MALDI mass spectrometer.

Computational methods for protein identification from mass spectrometry data

Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.

Matrix-assisted laser desorption/ionization signal enhancement of peptides by picolinamidination of amino groups

Picolinamidination of amino groups in peptides was carried out using ethyl picolinimidate tetrafluoroborate synthesized from picolinamide and triethyloxonium tetrafluoroborate. The N-terminal amino group as well as the epsilon-amino group of lysine were derivatized. The matrix-assisted laser desorption/ionization (MALDI) signal of a peptide was enhanced 20-35-fold upon picolinamidination depending on the number of amino groups derivatized. The signal enhancement effect is much higher than that of acetamidination or guanidination previously reported. Improved protein identification by mass mapping of the derivatized peptides was demonstrated.

Trends in sample preparation for classical and second generation proteomics

Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.

Achieving Augmented Limits of Detection for Peptides with Hydrophobic Alkyl Tags

The wide range of protein concentrations found in biological matrixes presents a formidable analytical challenge in proteomics experiments. It is predicted that low-abundance proteins are the likely clinically relevant targets in disease-based proteomics analyses. To effectively analyze low-abundance proteins by electrospray ionization mass spectrometry, limits of detection must be improved upon. Previous studies have demonstrated hydrophobicity is a main determinant of the electrospray ionization response. One would expect to improve the electrospray ionization response of a hydrophilic peptide by making it more hydrophobic, thus increasing the molecule's affinity for the surface of the electrospray droplet, thereby allowing the molecule to more effectively compete for charge. In this report, we demonstrate a strategy to increase the electrospray ionization response of cysteine-containing peptides with the addition of an octylcarboxyamidomethyl modification via alkylation chemistry, which we name the ALiPHAT strategy (augmented limits of detection for peptides with hydrophobic alkyl tags). We demonstrate the relative increase in electrospray ionization response of peptides with an octylcarboxyamidomethyl modification compared to carboxyamidomethyl-modified peptides upon LC-MS analysis. Furthermore, we show the octylcarboxyamidomethyl group does not fragment or undergo neutral loss during collision-induced dissociation. Collectively, our results demonstrate the feasibility of the octylcarboxyamidomethyl modification to improve limits of detection for cysteine-containing peptides.

Detection of in situ derivatized peptides in microbial biofilms by laser desorption 7.87 eV postionizaton mass spectrometry

A novel analytical method based on laser desorption postionization mass spectrometry (LDPI-MS) was developed to investigate the competence and sporulation factor-a pentapeptide of amino acid sequence ERGMT-within intact Bacillus subtilis biofilms. Derivatization of the neat ERGMT peptide with quinoline- and anthracene-based tags was separately used to lower the peptide ionization potential and permit direct ionization by 7.87-eV vacuum ultraviolet radiation. The techniques of mass shifting and selective ionization of the derivatized peptide were combined here to permit detection of ERGMT peptide within intact biofilms by LDPI-MS, without any prior extraction or chromatographic separation. Finally, imaging MS specific to the derivatized peptide was demonstrated on an intact biofilm using LDPI-MS. The presence of ERGMT in the biofilms was verified by bulk extraction/LC-MS. However, MALDI imaging MS analyses were unable to detect ERGMT within intact biofilms.