Scaling of skeletal mass to body mass in fishes

The few available observations are consistent with the supposition that the relative weightlessness of fishes leads to isometric scaling of skeletal mass to body mass. To explore further this pattern we studied scaling in ontogeny with freshwater tilapia, Oreochromis nilotica, and in phylogeny with adult coral reef fishes. Body mass and skeletal mass were measured for freshly caught fishes. Data were transformed to logarithms and fitted to a power function with least-square linear regression. Whereas slope for all O. nilotica combined was consistent with isometry (b = 1.00; 95% CI = 0.02), slopes calculated separately for juveniles (b = 1.16; CI = 0.07) and adults (b = 1.10; CI = 0.07) indicated positive allometric scaling of the skeleton during ontogeny. The scaling pattern was isometric for a multispecies sample of perciform fishes from coral reefs (b = 0.82; CI = 0.21). However, the single perciform species with the largest number of individuals in the sample, Epinephelus guttatus, was positively allometric (b = 1.13; CI = 0.12), whereas the tetraodontiform, Balistes vetula, was isometric (b = 1.05; CI = 0.12). Instead of leading to isometry, weightlessness may increase the range of possibilities for the scaling of skeleton mass to body mass in fishes compared to terrestrial vertebrates. The scaling of the skeleton in fishes may be related to foraging style and manner of locomotion in water rather than be driven by the need to resist gravity. © 1996 Wiley-Liss, Inc.     

Accurate mass analysis of phosphoramidites by electrospray mass spectrometry

A method of accurate mass determination of phosphoramidites is described. The commonly used methanol/water/acid system was replaced by LiCl-containing acetonitrile and the concentrations of LiCl, poly(ethylene glycol), and phosphoramidite samples were optimized.     

Charge variant native mass spectrometry benefits mass precision and dynamic range of monoclonal antibody intact mass analysis

ABSTRACT

The preponderance and diversity of charge variants in therapeutic monoclonal antibodies has implications for antibody efficacy and degradation. Understanding the extent and impact of minor antibody variants is of great interest, and it is also a critical regulatory requirement. Traditionally, a combination of approaches is used to characterize antibody charge heterogeneity, including ion exchange chromatography and independent mass spectrometric variant site mapping after proteolytic digestion. Here, we describe charge variant native mass spectrometry (CVMS), an integrated native ion exchange mass spectrometry-based charge variant analytical approach that delivers detailed molecular information in a single, semi-automated analysis. We utilized pure volatile salt mobile phases over a pH gradient that effectively separated variants based on minimal differences in isoelectric point. Characterization of variants such as deamidation, which are traditionally unattainable by intact mass due to their minimal molecular weight differences, were measured unambiguously by mass and retention time to allow confident MS1 identification. We demonstrate that efficient chromatographic separation allows introduction of the purified forms of the charge variant isoforms into the Orbitrap mass spectrometer. Our CVMS method allows confident assignment of intact monoclonal antibody isoforms of similar mass and relative abundance measurements across three orders of magnitude dynamic range.     

Evolutionary patterns from mass originations and mass extinctions

The Fossil Record 2 database gives a stratigraphic range of most known animal and plant families. We have used it to plot the number of families extant through time and argue for an exponential fit, rather than a logistic one, on the basis of power spectra of the residuals from the exponential. The times of origins and extinctions, when plotted for all families of marine and terrestrial organisms over the last 600 Myr, reveal different origination and extinction peaks. This suggests that patterns of biological evolution are driven by its own internal dynamics as well as responding to upsets from external causes. Spectral analysis shows that the residuals from the exponential model of the marine system are more consistent with 1/f noise suggesting that self-organized criticality phenomena may be involved.     

Enhanced peptide mass fingerprinting through high mass accuracy: Exclusion of non-peptide signals based on residual mass

Peptide mass fingerprinting (PMF) is among the principle methods of contemporary proteomic analysis. While PMF is routinely practiced in many laboratories, the complexity of protein tryptic digests is such that PMF based on unrefined mass spectrometric peak lists is often inconclusive. A number of data processing strategies have thus been designed to improve the quality of PMF peak lists, and the development of increasingly elaborate tools for PMF data reduction remains an active area of research. In this report, a novel and direct means of PMF peak list enhancement is suggested. Since the monoisotopic mass of a peptide must fall within a predictable range of residual values, PMF peak lists can in principle be relieved of many non-peptide signals solely on the basis of accurately determined monoisotopic mass. The calculations involved are relatively simple, making implementation of this scheme computationally facile. When this procedure for peak list processing was used, the large number of unassigned masses typical of PMF peak lists was considerably attenuated. As a result, protein identifications could be made with greater confidence and improved discrimination as compared to PMF queries submitted with raw peak lists. Importantly, this scheme for removal of non-peptide masses was found to conserve peptides bearing various post-translational and artificial modifications. All PMF experiments discussed here were performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which provided the high mass resolution and high mass accuracy essential for this application. Previously reported equations relating the nominal peptide mass to the permissible range of fractional peptide masses were slightly modified for this application, and these adjustments have been illustrated in detail. The role of mass accuracy in application of this scheme has also been explored.     

离子阱串联质谱仪质荷比测量误差统计分析

离子阱串联质谱仪是蛋白质组研究中一种高通量,高灵敏度的分析仪器。目前对影响离子阱质谱仪质荷比测量误差的因素和数据产出后系统误差的校正方法还没有系统的分析。利用两批蛋白质标准品的数据和统计方法分析了离子阱质谱仪质荷比测量误差的分布规律,对测量的质荷比和信号强度对测量误差的影响进行了分析。在此基础上,提出了一种对质谱数据进行系统误差再校正的方法和一种根据信号强度确定误差容限的模型。     

Numerical bias estimation for mass spectrometric mass isotopomer analysis

Mass spectrometric (MS) isotopomer analysis has become a standard tool for investigating biological systems using stable isotopes. In particular, metabolic flux analysis uses mass isotopomers of metabolic products typically formed from ¹³C-labeled substrates to quantitate intracellular pathway fluxes. In the current work, we describe a model-driven method of numerical bias estimation regarding MS isotopomer analysis. Correct bias estimation is crucial for measuring statistical qualities of measurements and obtaining reliable fluxes. The model we developed for bias estimation corrects a priori unknown systematic errors unique for each individual mass isotopomer peak. For validation, we carried out both computational simulations and experimental measurements. From stochastic simulations, it was observed that carbon mass isotopomer distributions and measurement noise can be determined much more precisely only if signals are corrected for possible systematic errors. By removing the estimated background signals, the residuals resulting from experimental measurement and model expectation became consistent with normality, experimental variability was reduced, and data consistency was improved. The method is useful for obtaining systematic error-free data from ¹³C tracer experiments and can also be extended to other stable isotopes. As a result, the reliability of metabolic fluxes that are typically computed from mass isotopomer measurements is increased.     

Questions of mass extinction

Earth's biodiversity is being overtaken by a mass extinction which, if allowed to proceed unchecked, could well eliminate between one quarter and one half of all species. Our conservation responses must be science-based if we are to address the problem in its full scope and with most productive use of conservation resources. Yet our scientific understanding of the impending mass extinction is inadequate in many salient respects. We have only a rudimentary grasp of the number of species at risk, of biodiversity depletion processes, of island biogeography in practice, and of evolutionary consequences, to cite but a few leading questions. The same applies to the issue of the most efficient strategies to confront the conservation challenge. Worse, there is scant evidence (due in part to gross lack of funding) of a comprehensive and coordinated campaign to mount a research effort of scope to match the problem. The paper broaches ten key questions that warrant urgent attention.     

Analysis of polyunsaturated aminophospholipid molecular species using isotope-tagged derivatives and tandem mass spectrometry/mass spectrometry/mass spectrometry

When aminophospholipids with only saturated and monounsaturated fatty acids esterified to the glycerol backbone were labeled with isotopically enriched N-methylpiperazine acetic acid N-hydroxysuccinimide ester reagents, it was found that they could be readily detected as N-methylpiperazine-amide-tagged aminophospholipids using a precursor scan of the stable isotope reporter ion (m/z 114-117) formed by tandem mass spectrometry/mass spectrometry. However, it was found in the current study that these precursor ion scans are not useful in determining the changes of aminophospholipids with polyunsaturated fatty acids (PUFAs) esterified to the glycerol backbone due to the presence of interfering ions in the reporter ion region. Therefore, a method was developed using tandem mass spectrometry/mass spectrometry/mass spectrometry (MS(3)) to obtain reporter ion ratios that were not distorted by interfering ions present in the collision-induced dissociation spectra of nontagged aminophospholipids with PUFAs. This new MS(3) method for N-methylpiperazine- amide-tagged aminophospholipids was used to examine the fate of diacyl, ether, or plasmalogen glycerophosphoethanolamine (GPEtn) species after exposure of human polymorphonuclear leukocytes to A23187 and granulocyte macrophage-colony-stimulating factor/formyl-methionyl-leucyl-phenylalanine stimuli, which can induce eicosanoid biosynthesis, to follow those GPEtn molecular species which were the source of arachidonic acid released. Upon stimulation of the human polymorphonuclear leukocyte, it was found that the abundant arachidonoyl GPEtn plasmalogen molecular species were uniquely reduced in relative content compared to ether or diacyl species and this subclass of GPEtn may be a source of the arachidonic acid converted to leukotrienes by the 5-lipoxygenase pathway activated in this cell.     

Weapons of mass retraction

Twitching motility is a unique form of bacterial propulsion on solid surfaces associated with cycles of extension, tethering and retraction of type IV pili (T4P). Although investigations over the last two decades in a number of species have identified the majority of the genes involved in this process, we are still learning how these pili are assembled and the mechanics by which bacteria use T4P to drag themselves from one place to another. Among the puzzles that remain to be solved is the mechanism by which hydrolysis of ATP is coupled to pilus assembly and disassembly, and how the cell envelope structure is modified to accommodate the passage of the pilus through the periplasm. Unravelling of these and other enigmas in the T4P system will not only teach us more about these important colonization and virulence factors, but also help us to understand related processes such as type II secretion, which relies on a set of proteins homologous to those in the T4P system, and bacterial conjugation, involving retractable pili belonging to the F-like subgroup of the type IV secretion family. This review focuses on recent discoveries relating to the assembly and function of T4P in generation of twitching motility.     

黎族人的瘦体与脂肪质量指数

2014年11月在海南省五指山市5个黎族村寨测量了607例(男为308例,女为299例)黎族人体质量、身高等6项体成分指标值,计算了黎族人的体脂率(P_(bf))、瘦体质量(m_l)、脂肪质量(m_f)、瘦体质量指数(I_(lm))、脂肪质量指数(I_(fm))。研究发现,女性体脂率、脂肪质量、脂肪质量指数都明显大于男性,瘦体质量、瘦体质量指数均明显小于男性。随年龄增长,黎族人身高、瘦体质量逐渐减小,体脂率、脂肪质量、脂肪质量指数逐渐增大。受试者特征曲线显示身体质量指数、脂肪质量指数都可以适宜评价黎族人的体脂率,而且脂肪质量指数对体脂率的估算准确性比身体质量指数更高。这也提示脂肪质量指数是比身体质量指数评价肥胖更好的指标。     

A platform for accurate mass and time analyses of mass spectrometry data

We describe an integrated suite of algorithms and software for general accurate mass and time (AMT) tagging data analysis of mass spectrometry data. The AMT approach combines identifications from liquid chromatography (LC) tandem mass spectrometry (MS/MS) data with peptide accurate mass and retention time locations from high-resolution LC-MS data. Our workflow includes the traditional AMT approach, in which MS/MS identifications are located in external databases, as well as methods based on more recent hybrid instruments such as the LTQ-FT or Orbitrap, where MS/MS identifications are embedded with the MS data. We demonstrate our AMT workflow's utility for general data synthesis by combining data from two dissimilar biospecimens. Specifically, we demonstrate its use relevant to serum biomarker discovery by identifying which peptides sequenced by MS/MS analysis of tumor tissue may also be present in the plasma of tumor-bearing and control mice. The analysis workflow, referred to as msInspect/AMT, extends and combines existing open-source platforms for LC-MS/MS (CPAS) and LC-MS (msInspect) data analysis and is available in an unrestricted open-source distribution.     

Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap

Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers are well controlled. Here we demonstrate sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap (C-trap) to the orbitrap mass spectrometer (LTQ Orbitrap). Prior to acquisition of a spectrum, a background ion originating from ambient air is first transferred to the C-trap. Ions forming the MS or MS(n) spectrum are then added to this species, and all ions are injected into the orbitrap for analysis. Real time recalibration on the "lock mass" by corrections of mass shift removes mass error associated with calibration of the mass scale. The remaining mass error is mainly due to imperfect peaks caused by weak signals and is addressed by averaging the mass measurement over the LC peak, weighted by signal intensity. For peptide database searches in proteomics, we introduce a variable mass tolerance and achieve average absolute mass deviations of 0.48 ppm (standard deviation 0.38 ppm) and maximal deviations of less than 2 ppm. For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching. High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.     

From mass customization to mass personalization: a strategic transformation

Business and operations strategists have long sought to formulate strategies that would serve profitably for a market of one. Two decades after its conception, there is growing evidence that mass customization strategy is transforming into a mass personalization strategy, making the market of one a reality, at least in select industries. The degree of transformation of a company depends on the extent to which its product is soft, i.e., can be produced electronically. Thus, at the lower end of the personalization spectrum are manufacturing companies engaged in producing hard, configurable products, while on the high end of the spectrum are service companies whose product can be totally configured and delivered electronically. The underlying factors that are enabling this transformation, in our view, are: (1) development of information technologies such as peer to peer (P2P), business to consumer (B2C), and Web 2.0, (2) near-universal availability of the Internet, (3) customer willingness and preparedness to be integrated into the process of product co-design and co-creation, (4) modern manufacturing systems, such as flexible manufacturing and, of course, (5) mass customization tools such as modularity and delayed differentiation, which help reduce manufacturing cost and cycle times and (6) deployment of customer-satisfaction-specific software called customer relationship management (CRM) to engender customer retention. Due to the importance and strategic success of affordable personalization, this issue is dedicated to that theme. The articles included in this issue would, I believe, serve as significant decision support mechanisms for companies pursuing a mass customization and personalization strategy. In addition to providing a brief perspective on articles included in this issue, we also summarize the state of the art of mass customization research.     

On mass behavior

In imitative behavior, as studied previously by N. Rashevsky (Mathematical Biology of Sociol Behavior, Chapter XIII, The University of Chicago Press, 1950), the reason for the majority of a society to accept a particular behavior is based on purely voluntary action (band-wagon effect). In the present paper effects of coercion of the majority by a small minority group which poses the means for coercion, are studied. More general types of equations are thus obtained and threshold effects found, which bear a resemblance to some such effects studied previously.