Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap

Precision proteomics requires high-resolution and high mass accuracy peptide measurements. The Orbitrap instrument achieves excellent resolution on a chromatographic time scale and its design is favorable for very high mass accuracy. Here we describe how mass precision for each peptide increases successively by considering all associated measurements, starting from the MS peak and proceeding to its chromatographic elution profile, isotope envelope, and stable isotope pair in SILAC measurements. We extract peptide charge pairs to perform nonlinear recalibration of the Orbitrap mass scale through spline interpolation. The deviation of mass values determined from charge pairs is used to convert mass precision to mass accuracy for subsequent database search. The corrected mass precision is consistent with the mass accuracy independently determined by database identification. Individual mass deviations range from below 100 ppb for peptides with many associated mass measurements and good signal intensities to low ppm for peptides with few mass measurements and signals close to the noise level. This extremely high and individualized mass accuracy is equivalent to a substantial increase in database identification score.     

An improved calibration method for the matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resononance analysis of 15N-metabolically- labeled proteome digests using a mass difference approach

High mass measurement accuracy of peptides in enzymatic digests is critical for confident protein identification and characterization in proteomics research. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) can provide low or sub-ppm mass accuracy and ultrahigh resolving power. While for ESI-FT-ICR-MS, the mass accuracy is generally 1 ppm or better, with matrix-assisted laser desorption/ionization (MALDI)-FT-ICR-MS, the mass errors can vary from sub-ppm with internal calibration to over 100 ppm with conventional external calibration. A novel calibration method for (15)N-metabolically labeled peptides from a batch digest of a proteome is described which corrects for space charge induced frequency shifts in FT-ICR spectra without using an internal calibrant. This strategy utilizes the information from the mass difference between the (14)N/(15)N peptide peak pairs to correct for space charge induced mass shifts after data collection. A procedure for performing the mass correction has been written into a computer program and has been successfully applied to high-performance liquid chromatography-MALDI-FT- ICR-MS measurement of (15)N-metabolic labeled proteomes. We have achieved an average measured mass error of 1.0 ppm and a standard deviation of 3.5 ppm for 900 peptides from 68 MALDI-FT-ICR mass spectra of the proteolytic digest of a proteome from Methanococcus maripaludis.     

Utility of three types of mass spectrometers for determining elemental compositions of ions formed from chromatographically separated compounds

Concentration factors of 1000 and more reveal dozens of compounds in extracts of water supplies. Library mass spectra for most of these compounds are not available, and alternative means of identification are needed. Determination of the elemental compositions of the ions in mass spectra makes feasible searches of commercial and chemical literature that often lead to compound identification. Instrumental capabilities that constrain the utility of a mass spectrometer for determining ion compositions for compounds that elute from a chromatographic column are scan speed, mass accuracy, linear dynamic range, and resolving power. Mass peak profiling from selected ion recording data (MPPSIRD) performed with a double-focusing mass spectrometer provides the best combination of these capabilities. This technique provides unique ion compositions for ions of higher mass from compounds eluting from a gas chromatograph than can be obtained by orthogonal acceleration time-of-flight (oa-TOF) or Fourier transform ion cyclotron resonance mass spectrometry. Multiple compositions are usually possible for an ion with a mass exceeding 150 Da within the error limits of the mass measurement. The correct composition is selected based on measured exact masses of the mass peak profiles resulting from isotopic ions higher in mass by 1 and 2 Da and accurate measurement of the summed abundances of these isotopic ions relative to the monoisotopic ion. A profile generation model (PGM) automatically determines which compositions are consistent with measured exact masses and relative abundances. The utility of oa-TOF and double-focusing mass spectrometry using ion composition elucidation (MPPSIRD plus the PGM) are considered for determining ion compositions of two compounds found in drinking water extracts and a third compound from a monitoring well at a landfill. Published in 2002 by John Wiley & Sons, Ltd.     

Intercomparison study on accurate mass measurement of small molecules in mass spectrometry

The results from an intercomparison of accurate mass measurement of a small molecule (molecular weight 475 Da) across a broad range of mass spectrometers are reported. The intercomparison was designed to evaluate the relative capabilities and the optimum methodology of the diverse range of mass spectrometers currently used to record accurate mass measurements. The data will be used as a basis for developing guidance on accurate mass measurement. The need for guidance has resulted from the continued growth in the use of accurate mass measurements for assignment of elemental formula in the chemical and biochemical industries. This has been fuelled by a number of factors and includes the rapid pace of instrument development, which has enabled accurate mass measurements to be made in a less costly, yet robust fashion. The data from the intercomparison will allow us to compare those protocols that produced excellent accuracy and precision with those that produced poorer accuracy and/or precision for each type of mass spectrometer. The key points for best practice will then be established from this comparison for each type of mass spectrometer and accurate mass measurement technique. A compound was sent to the participating laboratories (in the UK, Europe, and USA), the identity of which was not revealed. Each laboratory was asked to record a minimum of five repeat mass measurements of the molecular species using their local protocols and their preferred ionization technique or techniques. To the best of our knowledge there were no interfering (unresolved) ions that originated from the sample. A questionnaire was also completed with the experimental work. The information from the questionnaires was used to evaluate the protocols used to record the measurements. Forty-five laboratories have reported their results. To summarize the performance of mass spectrometers in the intercomparison, magnetic sector field mass spectrometers used in peak matching mode and FTMS reported the highest mean mass measurement accuracy (88 and 83%, respectively, achieved < or =1 ppm). Magnetic sector field mass spectrometers used in voltage scanning produced 60% of the mean mass measurements with accuracy < or =1 ppm. Magnetic sector field mass spectrometers used in magnet scanning modes, quadrupole-TOF and TOF instruments generally achieved mean mass measurement accuracy between 5 and 10 ppm. The two low resolution triple quadrupoles used in the inter-comparison produced mean mass measurement accuracy of <2 ppm. The precision of the data from each instrument and experiment type is an important consideration when evaluating their relative capabilities. Using both the precision and accuracy, it will be possible to define the uncertainty associated with the elemental formulae derived from accurate mass measurements. Therefore, a thorough statistical evaluation of the data is underway and will be presented in a subsequent publication.     

有机质谱学在蛇床子素、厚朴酚、和厚朴酚与鱼腥草素结构确定中的应用

有机质谱学在中药药效物质的结构确定中起到了至关重要的作用. 对中药药效物质质谱的确切解释需要对这些药效物质质谱的关键裂解规律有足够的了解. 应用有机质谱学规律对中药药效物质的结构确定进行了讨论. 这些中药的药效物质包括: 应用超临界二氧化碳从蛇床子中提取的蛇床子素和从厚朴中提取的厚朴酚与和厚朴酚; 应用水蒸汽蒸馏从鱼腥草中提取的鱼腥草素等. 具有较高丰度的质谱关键碎片峰 m/z 229 的出现是蛇床子素质谱的典型特征; 质谱关键碎片峰 m/z 169 的出现是鱼腥草素质谱的典型特征. 而质谱关键碎片峰 m/z 247 是否出现则是区分厚朴酚与和厚朴酚的质谱典型特征. 在此基础上, 尝试构建中药药效物质的有机质谱学平台.     

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.     

Performance optimisation of a new-generation orthogonal-acceleration quadrupole-time-of-flight mass spectrometer

Orthogonal-acceleration quadrupole time-of-flight (oa-QTOF) mass spectrometers, employed for accurate mass measurement, have been commercially available for well over a decade. A limitation of the early instruments of this type was the narrow ion abundance range over which accurate mass measurements could be made with a high degree of certainty. Recently, a new generation of oa-QTOF mass spectrometers has been developed and these allow accurate mass measurements to be recorded over a much greater range of ion abundances. This development has resulted from new ion detection technology and improved electronic stability or by accurate control of the number of ions reaching the detector. In this report we describe the results from experiments performed to evaluate the mass measurement performance of the Bruker micrOTOF-Q, a member of the new-generation oa-QTOFs. The relationship between mass accuracy and ion abundance has been extensively evaluated and mass measurement accuracy remained stable (+/-1.5 m m/z units) over approximately 3-4 orders of magnitude of ion abundance. The second feature of the Bruker micrOTOF-Q that was evaluated was the SigmaFit function of the software. This isotope pattern-matching algorithm provides an exact numerical comparison of the theoretical and measured isotope patterns as an additional identification tool to accurate mass measurement. The smaller the value, the closer the match between theoretical and measured isotope patterns. This information is then employed to reduce the number of potential elemental formulae produced from the mass measurements. A relationship between the SigmaFit value and ion abundance has been established. The results from the study for both mass accuracy and SigmaFit were employed to define the performance criteria for the micrOTOF-Q. This provided increased confidence in the selection of elemental formulae resulting from accurate mass measurements.     

Comparison of electron ionization mass spectra of some organic compounds (MW < 200 Da) recorded on mass spectrometers of various types

Low-resolution electron ionization mass spectra recorded on various types of mass spectrometers (time-of-flight, quadrupole, and three-dimensional ion trap) were compared. A model mixture of 10 organic compounds (MW < 200 Da) was analyzed by gas chromatography-mass spectrometry. Pure mass spectra of analytes were extracted using the AMDIS software. The best repeatability was achieved for the time-of-flight mass spectrometer. The mass spectra recorded by a quadrupole and a time-of-flight mass spectrometer were quite similar. In the case of these instruments, library search using a commercial mass spectral data base (NIST’05) gave satisfactory result for each analyte (rank 1 or 2 in the “hit list”; Match > 900). In some cases, the mass spectra of model compounds recorded by the ion trap mass spectrometer differed in intensity of certain mass spectral peaks (but not in the set of peaks) from the mass spectra presented in the library and from the experimental mass spectra recorded by the time-of-flight and quadrupole instruments.     

Characterization of ammonium chloride derivatives by salt clustering in electrospray mass spectrometry

Clustering of ammonium chloride salts was studied using an electrospray source to characterize the form, mono- vs. dihydrochloride, of organic compounds by mass spectrometry. This new way of taking advantage of cluster formation is applied to aminomethylacridines as their storage requires the synthesis of such derivatives. Both positive and negative cluster mass spectra were obtained and allowed the determination of the nature of the hydrochloride forms as the salt mass is straightforwardly derived from the mass of the cluster monomer, calculated from singly and multiply charged ion distributions. The identity of the counterion is confirmed from the mass of the ionic moieties in the clusters.     

新一代电感耦合等离子体质谱（ICP-MS）全谱同时测定技术

介绍了最新推出的全谱同时检测的电感耦合等离子体质谱(ICP-MS)仪器,它是目前市场上唯一的从6Li到238U质量范围同时测量的ICP质谱仪,实现了从时序扫描测量到全谱同时测量的新飞跃.其革命性技术的核心是双聚焦扇形场质谱仪与全新的能够同时俘获全部离子的检测器及其创新设计的离子透镜系统,展现出优越的性能和更广阔的应用前...     

337 nm matrix-assisted laser desorption/ionization of single aerosol particles.

Matrix-assisted laser desorption/ionization (MALDI) mass spectra were obtained from single particles injected directly into a time-of-flight mass spectrometer. Aerosol particles were generated at atmospheric pressure using a piezoelectric single-particle generator or a pneumatic nebulizer and introduced into the mass spectrometer through a series of narrow-bore tubes. Particles were detected by light scattering that was used to trigger a 337 nm pulsed nitrogen laser and the ions produced by laser desorption were mass separated in a two-stage reflectron time-of-flight mass spectrometer. MALDI mass spectra of single particles containing bradykinin, angiotensin II, gramicidin S, vitamin B(12) or gramicidin D were obtained at mass resolutions greater than 400 FWHM. For the piezoelectric particle generator, the efficiency of particle delivery was estimated to be approximately 0.02%, and 50 pmol of sample were consumed for each mass spectrum. For the pneumatic nebulizer, mass spectra could be obtained from single particles containing less than 100 amol of analyte, although the sample consumption for a typical mass spectrum was over 400 pmol.     

Electron ionization-tandem mass spectrometry of glycosphingolipids. I: The identiftcation of compound-specific sequence ions in the collision-induced dissociation spectra of the immonium ions of two isomeric hexaglycosylceramides

A permethylated-reduced hexaglycosylceramide in a complex glycolipid mixture isolated from a unique human tissue has been identified by using tandem mass spectrometry (MS/MS). The mass spectrum of this glycolipid mixture, obtained by using in-beam electron ionization, is very complex, and fragment ions derived from the hexaglycosylceramide cannot be distinguished from other ions. Tandem mass spectrometry using a four-sector mass spectrometer gave the mass spectrum of the immonium ion of the permethylated-reduced hexaglycosykeramide (m / z 1645.8), which is characteristic of its structure. Comparison of this MS/MS spectrum with those of two similarly derivatized blood group hexaglycosylceramide isomers permitted identification of the unknown glycolipid structure.     

同位素质谱和无机质谱

本文是《分析试验室》定期评述中“同位素质谱和无机质谱”的第四篇评述，评述的范围是１９９４年１１月至１９９６年１０月我国气体同位素质谱，热电离同位素质谱，加速器质谱，火花源质谱，电感耦合等离子体质谱，辉光放电质谱，同位素稀释质谱，二次离子质谱，激光共振电离子飞行时间质谱，电子探针，质子探针，激光探针和它们在地学，核科学，环境科学，材料学，计理学，医学和生命科学中的应用，引用文献１４９篇。     

Optimization of quartz tube pyrolysis atmospheric pressure ionization mass spectrometry for the generation of bacterial biomarkers

Experimental procedures were investigated to improve the efflux of biomolecule pyrolyzates from quartz tube pyrolysis under atmospheric pressure ionization mass spectrometry conditions. Heating regimes, airflows, and ion focusing parameters were optimized to increase the informative mass spectral signals generated from the pyrolysis of Gram-positive bacterial spores and vegetative cells. Dipicolinic acid (DPA) is found in 5-15% by weight in Gram-positive Bacillus spores, and the parameter optimization procedures provided an intense mass spectral signature of the m/z 168 protonated DPA molecule with a minimization of pyrolytic and ionization fragments. Moreover, mass spectral information from the optimization protocols yielded peaks and mass patterns characteristic of DNA and RNA nitrogen bases, protein diketopiperazines, and amino sugars.     

Gas chromatography and gas chromatography/mass spectrometry for the characterization of complex mixtures of large oligosaccharides

High temperature gas chromatography and gas chromatography/mass spectrometry are used in the characterization of complex natural mixtures of permethylated oligosaccharides released from proteins or lipids. The high resolution allows separation of isomeric compounds and the mass range extends to oligosac-charides around molecular mass 2000 daltons or 10 sugar residues for isomalto-oligosaccharides. The mass spectra of permethylated oligosaccharide alditols from mucin glycopeptides are very informative and the approach allows a simple and rapid characterization of these complex components.     

Importance of enhanced mass resolution in removing interferences when measuring volatile organic compounds in human blood by using purge-and-trap gas chromatography/mass spectrometry

The number of volatile organic compounds (VOCs) that can be purged from human blood is so great that they cannot be separated completely by capillary gas chromatography. As a result, the single-mass chromatograms used for quantitating the target compounds by mass spectrometry have many interferences at nominal (integer) mass resolution of a quadrupole mass spectrometer. The results of these interferences range from small errors in quantitation to completely erroneous results for the target VOCs. By using a magnetic sector mass spectrometer, these interferences at nominal mass can be removed at higher resolution by lowering the ion chromatogram windows around the masses of interest. At 3000 resolution (10% valley definition), unique single-ion chromatograms can be made for the quantitation ions of the target VOCs. Full-scan mass data are required to allow the identification of unknown compounds purged from the blood. By using isotope-dilution mass spectrometry, most target VOCs can be detected in the low parts per trillion range for a 10-mL quantity of blood from which the VOCs have been removed by a purge-and-trap method.     

Identification of Phosphorylated Human Peptides by Accurate Mass Measurement Alone

At sufficiently high mass accuracy, it is possible to distinguish phosphorylated from unmodified peptides by mass measurement alone. We examine the feasibility of that idea, tested against a library of all possible in silico tryptic digest peptides from the human proteome database. The overlaps between in silico tryptic digest phosphopeptides generated from known phosphorylated proteins (1-12 sites) and all possible unmodified human peptides are considered for assumed mass error ranges of ±10, ±50, ±100, ±1,000, and ±10,000 ppb. We find that for mass error ±50 ppb, 95% of all phosphorylated human tryptic peptides can be distinguished from nonmodified peptides by accurate mass alone through the entire nominal mass range. We discuss the prospect of on-line LC MS/MS to identify phosphopeptide precursor ions in MS1 for selected dissociation in MS2 to identify the peptide and site(s) of phosphorylation.     

Shell-side mass transfer of hollow fibre modules in osmotic distillation process

The effect of packing density of hollow fibre modules on mass transfer in the shell side of osmotic distillation process was studied. The osmotic distillation experiments were carried out with several modules of the packing densities ranging from 30.6 to 61.2%. It was found that the Reynolds number was a function of packing density and packing density affected mass transfer performance. The shell-side mass transfer coefficient increased with the brine velocity. The membrane permeability can be predicted from the experimental flux at the maximum brine velocity. The mass transfer correlation was proposed in order to determine the shell-side mass transfer coefficient in the randomly packed modules for osmotic distillation process. The empirical correlation proposed was fitted to the experimental results and it was found that the mass transfer coefficients calculated from the proposed correlation were in good agreement with those from the experimental data. Comparison of the results obtained from the proposed correlation with other correlations in the literature was discussed.     

Automatic internal calibration in liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry of protein digests

Accurately measured peptide masses can be used for large-scale protein identification from bacterial whole-cell digests as an alternative to tandem mass spectrometry (MS/MS) provided mass measurement errors of a few parts-per-million (ppm) are obtained. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) routinely achieves such mass accuracy either with internal calibration or by regulating the charge in the analyzer cell. We have developed a novel and automated method for internal calibration of liquid chromatography (LC)/FTICR data from whole-cell digests using peptides in the sample identified by concurrent MS/MS together with ambient polydimethylcyclosiloxanes as internal calibrants in the mass spectra. The method reduced mass measurement error from 4.3 +/- 3.7 ppm to 0.3 +/- 2.3 ppm in an E. coli LC/FTICR dataset of 1000 MS and MS/MS spectra and is applicable to all analyses of complex protein digests by FTICRMS.     

Rapid accurate mass desorption electrospray ionisation tandem mass spectrometry of pharmaceutical samples

Desorption electrospray ionisation (DESI) has been successfully combined with a hybrid quadrupole time-of-flight mass spectrometer to provide mass spectra and product ion mass spectra of active ingredients formulated in pharmaceutical tablets, gels and ointments. Accurate mass data has been obtained from the DESI mass spectra and of the product ion fragments of selected ions, greatly enhancing the selectivity and information content of the experiment. This accurate mass information only takes seconds to acquire since the DESI technique does not require any sample preparation or extraction prior to mass analysis.