Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification

We describe a new interface for a prototype quadrupole-quadrupole-time-of-flight (TOF) mass spectrometer (Centaur, Sciex) that allows rapid switching between electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) modes of operation. Instrument performance in both modes is comparable (i.e., resolution approximately 10,000 FWHM, mass accuracy <10 ppm, sensitivity approximately 1 fmol) because the ion source is decoupled from the TOF mass analyzer by extensive gas collisions in the quadrupole stages of the instrument. The capacity to obtain side-by-side high quality ESI and MALDI mass spectra from a single proteolytic mixture greatly facilitates the identification of proteins and elucidation of their primary structures. Improved strategies for protein identification result from this ability to measure spectra using both ionization modes in the same instrument and to perform MS/MS on singly charged as well as multiply charged ions. Examples are provided to demonstrate the utility and performance of the modified instrument.     

Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells

Numerous experimental factors are shown to significantly influence the spectra obtained when bacteria are analyzed by MALDI TOF/MS. Detailed investigation of the instrument parameters and sample preparation are all shown to influence the spectra. Of these, the preanalysis sample preparation steps incorporate the most important elements influencing the quality and reproducibility of the spectra. Some of the most important sample preparation factors include the method employed for sterilization, the type of matrix, the matrix solvent and concentration of cells in the matrix, as well as the type and concentration of acid added to the matrix. The effects of these parameters, as well as other aspects of sample preparation and the effects of several instrumental parameters on spectra are presented. Optimization and control of all experimental variables leads to a stable protocol for analysis of bacteria. The protocol employs a Nd:Yag laser and describes both sample handling and instrument conditions which consistently yield reproducible MALDI TOF mass spectra with greater than 25 peaks from both gram-positive and gram-negative bacteria.     

Application of electrospray mass spectrometry and matrix-assisted laser desorption ionization time-of-flight mass spectrometry for molecular weight assignment of peptides in complex mixtures

Electrospray mass spectrometry (ES/MS) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI/TOF/MS) were used to provide mass spectra from seven elapid snake venoms. Spectral interpretation was much simpler for MALDI/TOF/MS. ES/MS proved more useful for the provision of molecular weight data for very closely related peptides, but suppression of higher molecular weight compounds was seen to occur during flow injection analysis. MALDI/TOF/MS proved useful for providing a complete picture of the venom, but the low resolution led to obscuring of major ions, and the mass accuracy was poorer for known peptides. Suppression also occurred during MALDI/TOF/MS but could be overcome using alternative matrices because the spectra were very dependent on the choice of matrix. ES/MS and MALDI/TOF/MS provide complementary and confirmatory information such that for the anal sis of complex peptide mixtures (snake venoms), the use of both techniques is desirable.     

Comparison of MALDI‐TOF mass spectra with microsatellite length polymorphisms in Candida albicans

Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI‐TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI‐TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well‐characterized collection strains, using a Microflex^TM system and Biotyper^TM software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI‐TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra‐clade spectra recognition were unsuccessful. In conclusion, MALDI‐TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI‐TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory. Copyright © 2015 John Wiley & Sons, Ltd.     

Precision profiling and identification of human serum peptides using Fourier transform ion cyclotron resonance mass spectrometry

Many biomarker discovery studies are based on matrix-assisted laser desorption/ionisation (MALDI) peptide profiles. In this study, 96 human serum samples were analysed on a Bruker solariX(TM) MALDI Fourier transform ion cyclotron resonance (FTICR) system equipped with a 15 tesla magnet. Isotopically resolved peptides were observed in ultrahigh resolution FTICR profiles up to m/z 6500 with mass measurement errors (MMEs) of previously identified peptides at a sub-ppm level. For comparison with our previous platform for peptide profile mass analysis (i.e. Ultraflex II) the corresponding time-of-flight (TOF) spectra were obtained with isotopically resolved peptides up to m/z 3500. The FTICR and TOF systems performed rather similar with respect to the repeatability of the signal intensities. However, the mass measurement precision improved at least 10-fold in ultrahigh resolution data and thus simplified spectral alignment necessary for robust and quantitatively precise comparisons of profiles in large-scale clinical studies. From each single MALDI-FTICR spectrum an m/z-list was obtained with sub-ppm precision for all different species, which is beneficial for identification purposes and interlaboratory comparisons. Furthermore, the FTICR system allowed new peptide identifications from collision-induced dissociation (CID) spectra using direct infusion of reversed-phase (RP) C(18)-fractionated serum samples on an electrospray ionisation (ESI) source.     

A high-performance matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer with collisional cooling

A high-performance orthogonal time-of-flight (TOF) mass spectrometer was developed specifically for use in combination with a matrix-assisted laser desorption/ionization (MALDI) source. The MALDI source features an ionization region containing a buffer gas with variable pressure. The source is interfaced to the TOF section via a collisional focusing ion guide. The pressure in the source influences the rate of cooling and allows control of ion fragmentation. The instrument provides uniform resolution up to 18,000 FWHM (full width at half maximum). Mass accuracy routinely achieved with a single-point internal recalibration is below 2 ppm for protein digest samples. The instrument is also capable of recording spectra of samples containing compounds with a broad range of masses while using one set of experimental conditions and without compromising resolution or mass accuracy.     

Analysis of antioxidants in insulation cladding of copper wire: a comparison of different mass spectrometric techniques (ESI–IT,MALDI–RTOF and RTOF–SIMS)

Commercial copper wire and its polymer insulation cladding was investigated for the presence of three synthetic antioxidants (ADK STAB AO412S, Irganox 1010 and Irganox MD 1024) by three different mass spectrometric techniques including electrospray ionization–ion trap–mass spectrometry (ESI–IT–MS), matrix‐assisted laser desorption/ionization reflectron time‐of‐flight (TOF) mass spectrometry (MALDI–RTOF–MS) and reflectron TOF secondary ion mass spectrometry (RTOF–SIMS). The samples were analyzed either directly without any treatment (RTOF–SIMS) or after a simple liquid/liquid extraction step (ESI–IT–MS, MALDI–RTOF–MS and RTOF–SIMS). Direct analysis of the copper wire itself or of the insulation cladding by RTOF–SIMS allowed the detection of at least two of the three antioxidants but at rather low sensitivity as molecular radical cations and with fairly strong fragmentation (due to the highly energetic ion beam of the primary ion gun). ESI–IT‐ and MALDI–RTOF–MS‐generated abundant protonated and/or cationized molecules (ammoniated or sodiated) from the liquid/liquid extract. Only ESI–IT–MS allowed simultaneous detection of all three analytes in the extract of insulation claddings. The latter two so‐called ‘soft’ desorption/ionization techniques exhibited intense fragmentation only by applying low‐energy collision‐induced dissociation (CID) tandem MS on a multistage ion trap‐instrument and high‐energy CID on a tandem TOF‐instrument (TOF/RTOF), respectively. Strong differences in the fragmentation behavior of the three analytes could be observed between the different CID spectra obtained from either the IT‐instrument (collision energy in the very low eV range) or the TOF/RTOF‐instrument (collision energy 20 keV), but both delivered important structural information. Copyright © 2009 John Wiley & Sons, Ltd.     

金黄色葡萄球菌及其甲氧苯青霉素耐药性的MALDI-TOF MS鉴定

用MALDI－TOS MS细菌指纹图谱鉴定细菌，建立区分金黄色葡萄球菌甲氧苯青霉素耐药株和敏感株的MALDI－TOF MS分析方法，检测了76株从临床标本中分离得到的金黄色葡萄球菌，用软件进行聚类分析，以nuc(耐热核酸酶）基因和mecA(耐药）基因聚合酶链反应（PCR）检测结果为参照，74％的菌株经MALDI－TOF MS给出了正确的鉴定结果；金黄色葡萄球菌甲氧苯青霉素耐药株和敏感株的质谱图有很大差别，各自有其特征峰；经过软件聚类分析，76株实验菌株划敏感群和耐药群；与PCR检测结果对照，有7株菌PCR检测mecA基因为阴性，而经MALDI－TOF MS鉴定为耐药株，表型鉴定表明其中有5株为敏感株；利用细菌指纹图谱和数据库检索对大多数菌株实现了正确鉴定；MALDI－TOF MS分辨率高，甚至可以区分株间的差异，实现了区分金黄色葡萄球菌甲氧苯青霉素耐药株和敏感株；结果表明MALDI－TOF MS提供了一个很有前景的鉴定细菌的快速方法。     

Mass correlated acceleration in a reflectron MALDI TOF mass spectrometer: an approach for enhanced resolution over a broad mass range

Compared to continuous extraction, pulsed extraction (PE) of ions formed by matrix-assisted laser desorption/ionization (MALDI) in time-of-flight (TOF) mass spectrometers significantly improves mass resolution. Parameters such as extraction voltage, delay time, and correction pulse must be varied, however, to achieve optimum mass resolution over a broad mass range because the PE method is mass dependent. We previously reported a novel method, mass correlated acceleration (MCA), which we have now combined with a reflectron MALDI TOF mass spectrometer to further enhance mass resolution over a broader mass range. Unlike the PE method, MCA is not mass dependent and high resolution mass spectra can be achieved with a single tuning of instrument parameters. The ions may be brought into focus simultaneously, i.e., the multi-channel recording advantage can be more fully realized. The MCA dual-stage ion source design includes an extraction pulse region and an acceleration region that contains a time-dependent waveform correlated with mass. We demonstrate the validity of this novel technique with applications in peptide mixture analysis and protein digests of lysozyme and bovine serum albumin.     

基质辅助激光解吸电离飞行时间质谱研究（I）：林芳烃化合物

采用基质辅助激光解吸电离飞行时间质谱（ＭＡＬＤＩ－ＴＯＦ－ＭＳ）对杯芳烃化合物进行了分析。探讨了样品的制备条件、仪器操作参数等因素对测定结果的影响。２５种样品的质谱数据表明,利用ＭＡＬＤＩ－ＴＯＦ－ＭＳ可非常方便地得到灵敏度、分辨率、准确度均较高,且易于识别和解析的质谱图,为此类化合物的质谱表征提供和建立了一种新的高效分析方法。     

Spectral quality assessment and application for gel-based matrix-assisted laser desorption ionization-time of flight tandem mass spectrometer

Gel-based matrix-assisted laser desorption ionization-time of flight tandem mass spectrometer (MALDI TOF/TOF MS) is one of the dominant methods of current proteomics, utilizing both peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) for protein identification on a spot-to-spot basis. However, the unique impact of the quality of the corresponding mass spectrometry spectra remains largely unreported, and has motivated the development and use of an automatic spectra-assessment method. In this study, a multi-variant regression approach has been utilized to assess spectral quality for both PMF and PFF spectra obtained from MALDI TOF/TOF MS. The assessment index has been applied to investigations of MASCOT search results. Systematic examination of two large-scale sets of human liver tissue data has proved that spectral quality was a key factor in significant matching. Based on large-scale investigations on individual PMF search, individual PFF search and their combination, respectively, the filtering of bad quality spectra or spots proves to be an efficient way to improve search efficiency of all search modes in MASCOT. Meanwhile, a validation method based on score differences between normal and decoy (reverse or random) database searches is proposed to precisely define the positive matches. Further analysis showed that spectral quality assessment was also efficient in representing the quality of 2-DE gel spots and promoted the discovery of potential post-translation modifications.     

Characterization of covalently inhibited extracellular lipase from Streptomyces rimosus by matrix-assisted laser desorption/ionization time-of-flight and matrix-assisted laser desorption/ionization quadrupole ion trap reflectron time-of-flight mass spectrometry: localization of the active site serine

A chemical modification approach combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to identify the active site serine residue of an extracellular lipase from Streptomyces rimosus R6-554W. The lipase, purified from a high-level overexpressing strain, was covalently modified by incubation with 3,4-dichloroisocoumarin, a general mechanism-based serine protease inhibitor. MALDI time-of-flight (TOF) mass spectrometry was used to probe the nature of the intact inhibitor-modified lipase and to clarify the mechanism of lipase inhibition by 3,4-dichloroisocoumarin. The stoichiometry of the inhibition reaction revealed that specifically one molecule of inhibitor was bound to the lipase. The MALDI matrix 2,6-dihydroxyacetophenone facilitated the formation of highly abundant [M + 2H](2+) ions with good resolution compared to other matrices in a linear TOF instrument. This allowed the detection of two different inhibitor-modified lipase species. Exact localization of the modified amino acid residue was accomplished by tryptic digestion followed by low-energy collision-induced dissociation peptide sequencing of the detected 2-(carboxychloromethyl)benzoylated peptide by means of a MALDI quadrupole ion trap reflectron TOF instrument. The high sequence coverage obtained by this approach allowed the confirmation of the site specificity of the inhibition reaction and the unambiguous identification of the serine at position 10 as the nucleophilic amino acid residue in the active site of the enzyme. This result is in agreement with the previously obtained data from multiple sequence alignment of S. rimosus lipase with different esterases, which indicated that this enzyme exhibits a characteristic Gly-Asp-Ser-(Leu) motif located close to the N-terminus and is harboring the catalytically active serine residue. Therefore, this study experimentally proves the classification of the S. rimosus lipase as GDS(L) lipolytic enzyme.     

High‐resolution MALDI‐TOF MS study on analysis of low‐molecular‐weight products from photo‐oxidation of poly(3‐hexylthiophene)

High‐resolution matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight mass spectrometry (TOF MS) was used for the analysis of the low‐molecular‐weight products from the photo‐oxidation of poly(3‐hexylthiophene) (P3HT) in solution and thin film. Eight new peak series were observed in the low‐mass range of the mass spectra of the products degraded in solution, and the formulas of the eight components were determined from the accurate mass. From SEC/MALDI‐TOF MS, two components were identified as the degraded products, and the other six components were derived from the fragmentation of the degraded products during the MALDI process. A mechanism for the formation of these components was proposed on the basis of the results of MALDI‐TOF MS. For the thin film degradation, a part of products in the solution degradation were observed, which supports that the oxidation of P3HT in solution and thin film proceeded in the same mechanism. This study shows that high‐resolution MALDI‐TOF MS is effective for the analysis of the low‐molecular‐weight products from P3HT photo‐oxidation and expected to be feasible for the degradation analyses of other polymers. Copyright © 2015 John Wiley & Sons, Ltd.     

De novo peptide sequencing using exhaustive enumeration of peptide composition

We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.     

A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics

A new matrix-assisted laser-desorption/ionization time-of-flight/time-of-flight mass spectrometer with the novel "LIFT" technique (MALDI LIFT-TOF/TOF MS) is described. This instrument provides high sensitivity (attomole range) for peptide mass fingerprints (PMF). It is also possible to analyze fragment ions generated by any one of three different modes of dissociation: laser-induced dissociation (LID) and high-energy collision-induced dissociation (CID) as real MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique. Fully automated operation including spot picking from 2D gels, in-gel digestion, sample preparation on MALDI plates with hydrophilic/hydrophobic spot profiles and spectrum acquisition/processing lead to an identification rate of 66% after the PMF was obtained. The workflow control software subsequently triggered automated acquisition of multiple MS/MS spectra. This information, combined with the PMF increased the identification rate to 77%, thus providing data that allowed protein modifications and sequence errors in the protein sequence database to be detected. The quality of the MS/MS data allowed for automated de novo sequencing and protein identification based on homology searching.     

Phosphorylated serine and threonine residues promote site‐specific fragmentation of singly charged,arginine‐containing peptide ions

In order to investigate gas‐phase fragmentation reactions of phosphorylated peptide ions, matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass (MS/MS) spectra were recorded from synthetic phosphopeptides and from phosphopeptides isolated from natural sources. MALDI‐TOF/TOF (TOF: time‐of‐flight) spectra of synthetic arginine‐containing phosphopeptides revealed a significant increase of y ions resulting from bond cleavages on the C‐terminal side of phosphothreonine or phosphoserine. The same effect was found in ESI‐MS/MS spectra recorded from the singly charged but not from the doubly charged ions of these phosphopeptides. ESI‐MS/MS spectra of doubly charged phosphopeptides containing two arginine residues support the following general fragmentation rule: Increased amide bond cleavage on the C‐terminal side of phosphorylated serines or threonines mainly occurs in peptide ions which do not contain mobile protons. In MALDI‐TOF/TOF spectra of phosphopeptides displaying N‐terminal fragment ions, abundant b–H₃PO₄ ions resulting from the enhanced dissociation of the pSer/pThr–X bond were detected (X denotes amino acids). Cleavages at phosphoamino acids were found to be particularly predominant in spectra of phosphopeptides containing pSer/pThr–Pro bonds. A quantitative evaluation of a larger set of MALDI‐TOF/TOF spectra recorded from phosphopeptides indicated that phosphoserine residues in arginine‐containing peptides increase the signal intensities of the respective y ions by almost a factor of 3. A less pronounced cleavage‐enhancing effect was observed in some lysine‐containing phosphopeptides without arginine. The proposed peptide fragmentation pathways involve a nucleophilic attack by phosphate oxygen on the carbon center of the peptide backbone amide, which eventually leads to cleavage of the amide bond. Copyright © 2009 John Wiley & Sons, Ltd.     

Solvent selection for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric analysis of synthetic polymers employing solubility parameters

The principle relating to the selection of a proper matrix, cationization reagent, and solvent for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) of synthetic polymers is still a topic of research. In this work we focused on the selection of a suitable MALDI solvent. Polystyrene PS7600 and poly(ethylene glycol) PEG4820 were analyzed by MALDI‐TOF MS using various solvents which were selected based on the Hansen solubility parameter system. For polystyrene (PS), dithranol was used as the matrix and silver trifluoroacetate as the cationization reagent whereas, for poly(ethylene glycol) (PEG), the combination of 2,5‐dihydroxybenzoic acid and sodium trifluoroacetate was used for all experiments. When employing solvents which dissolve PS and PEG, reliable MALDI mass spectra were obtained while samples in non‐solvents (solvents which are not able to dissolve the polymer) failed to provide spectra. It seems that the solubility of the matrix and the cationization reagent are less important than the polymer solubility. Copyright © 2010 John Wiley & Sons, Ltd.     

基质辅助激光解吸电离飞行时间质谱研究2: 四硫 富瓦烯化合物

采用基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS),对四硫富瓦烯化合物进行质谱表征。在所用的实验条件下,样品很容易解吸电离生成单电荷分子离子,得到单同位素分辨的质谱图。26种实际样品的质谱分析结果表明;MALDI-TOF-MS可以比其它质谱方法更有效、更方便地用于此类化合物的质谱分析,解决了此类化合物不易进行质谱鉴定的难题。     

Reflectron MALDI TOF and MALDI TOF/TOF mass spectrometry reveal novel structural details of native lipooligosaccharides

Lipooligosaccharides (LOS) are powerful Gram-negative glycolipids that evade the immune system and invade host animal and vegetal cells. The structural elucidation of LOS is pivotal to understanding the mechanisms of infection at the molecular level. The amphiphilic nature of LOS has been the main obstacle for structural analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Our approach has resolved this important issue and has permitted us to obtain reflectron MALDI mass spectra of LOS to reveal the fine chemical structure with minimal structural variations. The high-quality MALDI mass spectra show LOS species characteristic of molecular ions and defined fragments due to decay in the ion source. The in-source decay yields B-type ions, which correspond to core oligosaccharide(s), and Y-type ions, which are related to lipid A unit(s). MALDI tandem time-of-flight (TOF/TOF) MS of lipid A allowed for the elucidation of its structure directly from purified intact LOS without the need for any chemical manipulations. These findings constitute a significant advancement in the analysis of such an important biomolecule by MALDI MS.     

Rapid MALDI‐TOF molecular imaging: Instrument enhancements and their practical consequences

A new high performance linear MALDI‐TOF mass spectrometer provides both high spatial resolution and high speed. This instrument employs a new ion optics system with a grounded ion source and efficient transfer and detection of ions over a broad mass range. This provides very high sensitivity, precision, and an extended dynamic range for both positive and negative ion detection. Here we demonstrate the capabilities of this system by imaging pancreatic tissue samples from rats and mice.