Peptide and protein identification by matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay time-of-flight mass spectrometry

The potential of matrix-assisted laser desorption ionization (MALDI) and MALDI-post-source decay (PSD) time-of-flight mass spectrometry for the characterization of peptides and proteins is discussed. Recent instrumental developments provide for levels of sensitivity and accuracy that make these techniques major analytical tools for proteome analysis. New software developments employing protein database searches have greatly enhanced the fields of application of MALDI-PSD. Peptides and proteins can be easily identified even if only a partial sequence information is determined. Derivatization procedures have been optimized for MALDI-PSD to increase the structural information and to obtain a complete peptide sequence even in critical cases. They are fast, simple and can be performed on target. MALDI-PSD is also a very powerful tool to characterize or elucidate post-translational or chemically induced modifications. In association with database searches, proteins issued from electrophoretic gels can be identified after specific enzymatic cleavages and peptide mapping.     

Analysis of erlotinib and its metabolites in rat tissue sections by MALDI quadrupole time-of-flight mass spectrometry

A qualitative and quantitative analysis of erlotinib (RO0508231) and its metabolites was carried out on rat tissue sections from liver, spleen and muscle. Following oral administration at a dose of 5 mg/kg, samples were analyzed by matrix-assisted laser desorption ionization (MALDI) with mass spectrometry (MS) using an orthogonal quadrupole time-of-flight instrument. The parent compound was detected in all tissues analyzed. The metabolites following drug O-dealkylation could also be detected in liver sections. Sinapinic acid (SA) matrix combined with the dried-droplet method resulted in better conditions for our analysis on tissues. Drug quantitation was investigated by the standard addition method and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis on the tissue extracts. The presence of the parent compound and of its O-demethylated metabolites was confirmed in all tissue types and their absolute amounts calculated. In liver the intact drug was found to be 3.76 ng/mg tissue, while in spleen and muscle 6- and 30-fold lower values, respectively, were estimated. These results were compared with drug quantitation obtained by whole-body autoradiography, which was found to be similar. The potential for direct quantitation on tissue sections in the presence of an internal standard was also investigated using MALDI-MS. The use of alpha-cyano-4-hydroxycinnamic acid (CHCA) as the matrix resulted in better linearity for the calibration curves obtained with reference solutions of the drug when compared to SA, but on tissue samples no reliable quantitative analysis was possible owing to the large variability in the signal response. MS imaging experiments using MALDI in MS/MS mode allowed visualizing the distribution of the parent compound in liver and spleen tissues. By calculating the ratio between the total ion intensities of MS images for liver and spleen sections, a value of 6 : 1 was found, which is in good agreement with the quantitative data obtained by LC-MS/MS analysis.     

A strategy for direct identification of protein S-nitrosylation sites by quadrupole time-of-flight mass spectrometry

S-nitrosylation of proteins serves an important role in regulating diverse cellular processes including signal transduction, DNA repair, and neurotransmission. Identification of S-nitrosylation sites is crucial for understanding the significance of this post-translational modification (PTM) in modulating the function of a protein. However, it is challenging to identify S-nitrosylation sites directly by mass spectrometric (MS) methods due to the labile nature of the S-NO bond. Here we describe a strategy for direct identification of protein S-nitrosylation sites in an electrospray ionization (ESI) quadrupole time-of-flight (QTOF) mass spectrometer without prior chemical derivatization of S-nitrosylated peptides. Both sample buffer composition and MS hardware parameters were carefully adjusted to ensure that S-nitrosylated peptide ions could be analyzed by the QTOF MS with optimal signal/noise ratios. It was crucial that the proteins were preserved in a sample solution containing 1 mM EDTA and 0.1 mM neocuproine at neutral pH. Proteins dissolved in this solution are amenable to in-solution tryptic digestion, which is important for the analysis of biological samples. S-nitrosylated peptides were effectively analyzed by LC/MS/MS on QTOF MS, with an optimized cone voltage of 20 V and collision energy of 4 V. We have successfully applied this method to thioredoxin, a key antioxidant protein, and identified within it an S-nitrosylation site at Cys73.     

Mass spectrometric approaches for the characterization of proteins on a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer

This study demonstrates structural and conformational characterization of proteins by nanoflow electrospray ionization (nanoESI) mass spectrometry (MS) and tandem mass spectrometry (MS/MS) utilizing a quadrupole time-of-flight (Q-TOF) mass spectrometer (Micromass, Manchester, England). Model peptides were successfully sequenced at the 35 attomole (amol) level, and peptides derived from a tryptic in-gel digest of 25 femtomole (fmol) bovine serum albumin (BSA) were successfully sequenced. The results demonstrated that the MS/MS sensitivity of the Q-TOF clearly surpassed the detection limit of the silver stain. A silver destaining step greatly improved the mass analysis of peptides derived from in-gel digests. Interestingly, sequence analysis revealed BSA residue 424 (tyrosine) as a potential chlorination site. In addition, a modified procedure was successfully used to extract and measure the masses of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-resolved proteins in the 10-68.5 kDa range. The Q-TOF was also used to monitor conformational changes of proteins. These experiments demonstrated an acid-induced denaturation of BSA in the pH 3-4 range, and heat-induced unfolding of cytochrome c between 50 and 60 degrees C. Finally, Zn2+ binding was demonstrated for the carbonic anhydrase apoprotein. In summary, the wide range of applications and the high quality of the experimental data made the Q-TOF mass spectrometer a powerful analytical tool for protein characterization.     

A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation

A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H3PO4) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation.     

Selection of internal standards for quantitative analysis by matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry

The selection of an appropriate internal standard (IS) for quantification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is critical for the successful application of quantitative MALDI. Selection of the IS depends on the chemical similarity of the analyte and IS and the mass separation of the analyte and IS as a function of instrumental peak resolution. For the quantification of bovine insulin, a series of internal standards including horse heart cytochrome C, bovine insulin chain B, des-pentapeptide human insulin, and des-octapeptide porcine insulin was investigated. Des-pentapeptide human insulin was found to be the most appropriate internal standard (relative standard deviation of the standard curve slope = 2.99%, correlation coefficient = 0.988 in the range of 0.5-0.4 μmol/L). Two methods for measuring of the MALDI signal intensity were evaluated, direct peak integration following subtraction of a linear background and non-linear least squares curve fitting. The results obtained with these methods were equivalent.     

Selection of internal standards for quantitative analysis by matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry

 The selection of an appropriate internal standard (IS) for quantification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is critical for the successful application of quantitative MALDI. Selection of the IS depends on the chemical similarity of the analyte and IS and the mass separation of the analyte and IS as a function of instrumental peak resolution. For the quantification of bovine insulin, a series of internal standards including horse heart cytochrome C, bovine insulin chain B, des-pentapeptide human insulin, and des-octapeptide porcine insulin was investigated. Des-pentapeptide human insulin was found to be the most appropriate internal standard (relative standard deviation of the standard curve slope=2.99%, correlation coefficient=0.988 in the range of 0.5–0.4 μmol/L). Two methods for measuring of the MALDI signal intensity were evaluated, direct peak integration following subtraction of a linear background and non-linear least squares curve fitting. The results obtained with these methods were equivalent. Received: 10 November 1995 / Revised: 4 March 1996 / Accepted: 6 March 1996     

Characterization of pyrene end-labeled poly(ethylene glycol) by high resolution MALDI time-of-flight mass spectrometry

We report the characterization of a sample of poly(ethylene glycol) (PEG, M _n = 3841, M _w/M _n = 1.01), and its derivative end-labeled with pyrenebutyrate groups, using high resolution MALDI time-of-flight mass spectrometry. A matrix of 2-(4-hydroxyphenyl-azo)benzoic acid containing a trace of either sodium chloride or potassium chloride was employed for laser desorption. Peaks due to the sodium or potassium cationized polymers were obtained, equally spaced at 44 mass units apart. For the pyrenebutyrate diester, the analysis shows that 80 ± 2% of the chains were doubly labeled, with the ramaining chains containing only a single pyrene group. Molecular weight determinations for both sets of samples were entirely consistent with size-exclusion chromatography measurements, but were obtained with greater accuracy and less ambiguity about the influence of the end groups on the hydrodynamic radius of the polymer.     

Characterization of phosphopeptides from protein digests using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanoelectrospray quadrupole time-of-flight mass spectrometry

A two-step mass spectrometric method for characterization of phosphopeptides from peptide mixtures is presented. In the first step, phosphopeptide candidates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) based on their higher relative intensities in negative ion MALDI spectra than in positive ion MALDI spectra. The detection limit for this step was found to be 18 femtomoles or lower in the case of unfractionated in-solution digests of a model phosphoprotein, beta-casein. In the second step, nanoelectrospray tandem mass (nES-MS/MS) spectra of doubly or triply charged precursor ions of these candidate phosphopeptides were obtained using a quadrupole time-of-flight (Q-TOF) mass spectrometer. This step provided information about the phosphorylated residues, and ruled out nonphosphorylated candidates, for these peptides. After [(32)P] labeling and reverse-phase high-performance liquid chromatography (RP-HPLC) to simplify the mixtures and to monitor the efficiency of phosphopeptide identification, we used this method to identify multiple autophosphorylation sites on the PKR-like endoplasmic reticulum kinase (PERK), a recently discovered mammalian stress-response protein.     

Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry

Recent work on protein and peptide biomarker patterns revealed the difficulties in identifying their molecular components, which is indispensable for validation of the biological context. Cerebrospinal fluid and brain tissue are used as sources to discover new biomarkers, e.g. for neurodegenerative diseases. Many of these biomarker candidates are peptides with a molecular mass of <10 kDa. Their identification is favourably achieved with a 'top-down' approach, because this requires less purification and an enzymatic cleavage will often not yield enough specific fragments for successful database searches. Here, we describe an approach using quadrupole time-of-flight mass spectrometry (TOFMS) as a highly efficient mass spectrometric purification and identification tool after off-line decomplexation of biological samples by liquid chromatography. After initial peptidomic screening with matrix-assisted laser desorption/ionization (MALDI) TOFMS, the elution behaviour in chromatography and the exact molecular mass were used to locate the same signals in nanoelectrospray measurements. Most of the peaks detected in MALDI-TOFMS could be retrieved in nanoelectrospray quadrupole TOFMS. Suitable collision energies for informative fragment spectra were investigated for different parent ions, charge states and molecular masses. After collision-induced dissociation, the resulting fragmentation data of multiply charged ions can become much more complicated than those derived from tryptic peptide digests. However, the mass accuracy and resolution of quadrupole TOF instruments results in high-quality data suitable for determining peptide sequences. The protein precursor, proteolytic processing and post-translational modifications were identified by automated database searches. This is demonstrated by the exemplary identifications of thymosin beta-4 (5.0 kDa) and NPY (4.3 kDa) from rat hypothalamic tissue and ubiquitin (8.6 kDa) from human cerebrospinal fluid. The high data quality should also allow for de novo identification. This methodology is generally applicable for peptides up to a molecular mass of about 10 kDa from body fluids, tissues or other biological sources.     

Correction of accurate mass measurement for target compound verification by quadrupole time-of-flight mass spectrometry

The aim of this work is to evaluate quadrupole/time-of-flight (QTOF) mass spectrometry for simultaneous measurement of accurate mass and quantification of a target by using a stable isotopically labeled internal standard. Mixtures of caffeine and (13)C(3)-caffeine (internal standard) at different concentration ratios were analyzed by capillary HPLC/QTOF. A calibration plot for quantification is linear over a factor of 20. Without invoking any correction scheme, the mass accuracy seriously degraded when the ratio of the mass standard to the test compound was not unity. The accuracy could be restored to approximately 2 ppm by using a quadratic function to correct the measured mass as a function of the measured signal ratio of target and internal calibrant.     

Hydrogen atom scrambling in selectively labeled anionic peptides upon collisional activation by MALDI tandem time-of-flight mass spectrometry

We have previously shown that peptide amide hydrogens undergo extensive intramolecular migration (i.e., complete hydrogen scrambling) upon collisional activation of protonated peptides (Jørgensen et al. J. Am. Chem. Soc. 2005, 127, 2785–2793). The occurrence of hydrogen scrambling enforces severe limitations on the application of gas-phase fragmentation as a convenient method to obtain information about the site-specific deuterium uptake for proteins and peptides in solution. To investigate whether deprotonated peptides exhibit a lower level of scrambling relative to their protonated counterparts, we have now measured the level of hydrogen scrambling in a deprotonated, selectively labeled peptide using MALDI tandem time-of-flight mass spectrometry. Our results conclusively show that hydrogen scrambling is prevalent in the deprotonated peptide upon collisional activation. The amide hydrogens (¹H/²H) have migrated extensively in the anionic peptide, thereby erasing the original regioselective deuteration pattern obtained in solution.     

X-ray ionization and fragmentation for use with time-of-flight mass spectrometry

In this paper, we introduce laser desorption X-ray ionization for producing ions from the previously undetected neutral species present during laser desorption mass spectrometry. Studies involving the laser desorption of simple sugars were conducted to illustrate the differences between spectra with and without the X-ray source. Ionization was made possible by placing a 200 mCi Am X-ray source directly into the ionization chamber of a time-of-flight mass spectrometer.     

Laser desorption ionization and MALDI time-of-flight mass spectrometry for low molecular mass polyethylene analysis

Polyethylene's inert nature and difficulty to dissolve in conventional solvents at room temperature present special problems for sample preparation and ionization in mass spectrometric analysis. We present a study of ionization behavior of several polyethylene samples with molecular masses up to 4000 Da in laser desorption ionization (LDI) time-of-flight mass spectrometers equipped with a 337 nm laser beam. We demonstrate unequivocally that silver or copper ion attachment to saturated polyethylene can occur in the gas phase during the UV LDI process. In LDI spectra of polyethylene with molecular masses above approximately 1000 Da, low mass ions corresponding to metal-alkene structures are observed in addition to the principal distribution. By interrogating a well-characterized polyethylene sample and a long chain alkane, C94H190, these low mass ions are determined to be the fragmentation products of the intact metal-polyethylene adduct ions. It is further illustrated that fragmentation can be reduced by adding matrix molecules to the sample preparation.     

Alkali-hydroxide-doped matrices for structural characterization of neutral underivatized oligosaccharides by MALDI time-of-flight mass spectrometry

We report new approaches using alkali-hydroxide-doped matrices to facilitate structural characterization of neutral underivatized oligosaccharides by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) MS. The approaches involved pretreatment of the analytes with NaOH or LiOH in aqueous solution, followed by mixing them with MALDI matrices prior to MS analysis. It was found that for open-ended neutral underivatized oligosaccharides partial alkaline degradation occurred upon laser desorption and ionization of the hydroxide-pretreated analytes in 2,5-dihydroxybenzoic acid (DHBA). The effect intensified when nonacidic compounds such as 2,4,6-trihydroxyacetophenone (THAP) and 5-amino-2-mercapto-1,3,4-thiadiazole (AMT) were used as matrix. The degradation allowed facile identification of the reducing end residue of the analyte and facilitated its structural characterization by postsource decay TOF-MS. Applying the same technique using matrices composed of LiOH and THAP or AMT led to the production of singly as well as multiple lithiated ions of oligosaccharides containing hexoses with free 3-OH groups. Extensive lithiation through multiple hydrogen-lithium exchanges up to 6 Li atoms was observed for maltoheptaose, beta-cyclodextrin, and dextran 1500. Such a 'lithium tagging' technique makes it possible to differentiate positional isomers of milk-neutral oligosaccharides, lacto-N-difucohexaose I and II (LNDFH-I and LNDFH-II), without the need of chemical derivatization or tandem MS analysis.     

A fragmentation study of dihydroquercetin using triple quadrupole mass spectrometry and its application for identification of dihydroflavonols in Citrus juices

A mass spectrometric method using electrospray ionization with triple quadrupole and quadrupole time‐of‐flight hybrid (Q‐Tof) mass spectrometry has been applied to the structural characterization of dihydroflavonols. This family of compounds has been studied by liquid chromatography/tandem mass spectrometry (LC/MS/MS) for the first time in this work. A comprehensive study of the product ion MS spectra of the [M+H]⁺ ion of a commercially available standard has been performed. The most useful fragmentations in terms of structural identification are those that involve cleavage of the C‐ring, resulting in diagnostic ions of dihydroflavonol family: ^1,3A, ^1,2B, ^1,2B‐CO, ^0,2A, ^0,2A‐H₂O, ^0,2A‐CO, and ^0,2A‐H₂O‐CO, that allow the characterization of the substituents in the A‐ and B‐rings. In addition to those ions, other product ions due to losses of H₂O and CO molecules from the Y ion were observed. Their fragmentation mechanisms and ion structures have been proposed. The established fragmentation patterns have been used to successfully identity three dihydroflavonols found in tangerine juices for the first time. Copyright © 2009 John Wiley & Sons, Ltd.     

Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography–electrospray ionization–tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.     

Data requirements for protein identification using chemically-assisted fragmentation and tandem mass spectrometry

Many laboratories identify proteins by searching tandem mass spectrometry data against genomic or protein sequence databases. These database searches typically use the measured peptide masses or the derived peptide sequence and, in this paper, we focus on the latter. We study the minimum peptide sequence data requirements for definitive protein identification from protein sequence databases. Accurate mass measurements are not needed for definitive protein identification, even when a limited amount of sequence data is available for searching. This information has implications for the mass spectrometry performance (and cost), data base search strategies and proteomics research.     

Molecular structure of fulvic acids by electrospray with quadrupole time-of-flight mass spectrometry

Characterisation of the molecular structure of aquatic fulvic acids (FA) has been performed using a quadrupole time-of-flight (Q-TOF) mass spectrometer equipped with an electrospray ionisation interface. Molecular masses centred around 450 Da and sinusoidal spectral distributions have been obtained for all fulvic acids. Tandem mass spectrometry (MS/MS) experiments showed losses of 18 Da (H(2)O) and 44 Da (CO(2)), and possible molecular structures were determined for the first time to our knowledge. A methodology is reported for evaluating the average elemental composition of FA from high-resolution mass spectra by processing post-acquisition data calculations using molecular size distributions and atomic compositions of ions. The results are found to be consistent with elemental analysis data.     

Characterization of synthetic nucleic acids by electrospray ionization quadrupole time-of-flight mass spectrometry

The potential of electrospray ionization quadrupole-quadrupole-time-of-flight mass spectrometry (ESI-QqTOF-MS) for the characterization of synthetic nucleic acids was evaluated. Oligonucleotides ranging in size from 12 up to 51 nucleotides were analyzed via direct infusion MS as well as via liquid chromatography (LC) online hyphenated to MS. These experiments proved the outstanding mass spectrometric performance of the TOF mass analyzer in regard of accuracy, reproducibility, resolution, and sensitivity. During a 1-min run, the monoisotopic mass of (dT)(24) was measured with a maximum relative mass deviation of 7.64 ppm proving the high mass accuracy of the TOF analyzer. Over a period of 1 h, mean deviations were determined in the range between -3.58 ppm and 3.06 ppm demonstrating the high stability of the applied external calibration. The molecular mass of a 51-mer was measured with a deviation smaller than 3.23 ppm from the theoretical value. The resolution exceeded a value of m/Deltam = 20 000 (m is the measured mass and Deltam the full peak width at half-maximum), which enabled the separation of the isotopic peaks of all investigated oligonucleotides. Because of the outstanding transmission and detection efficiency of the TOF mass analyzer, detection limits in the amol/microl to low fmol/microl range were reached. The usability of LC-ESI-QqTOF-MS for the qualitative and quantitative analysis of synthetic oligonucleotide mixtures was demonstrated.