质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

Synthesis of deoxynivalenol-glucosides and their characterization using a QTrap LC-MS/MS

Deoxynivalenol (DON)-glucosides were successfully synthesized in a two-step reaction from 1-β-Bromo-1-deoxy-2,3,4,6-tetra-O-acetyl-α-D-gluco-pyranose and 3-Acetyl-DON or 15-Acetyl-DON. After purification of the reaction products, the mycotoxin conjugates were for the first time characterized by means of a triple quadrupole mass spectrometer in combination with a linear ion trap. Due to different fragmentation behaviour it was also possible to distinguish between the two glucosides. Presented at the 25^th Mykotoxin Workshop in Giessen, Germany, May 19–21, 2003     

A Novel Method for Relative Quantitation of N-Glycans by Isotopic Labeling Using 18O-Water

Quantitation is an essential aspect of comprehensive glycomics study. Here, a novel isotopic-labeling method is described for N-glycan quantitation using ¹⁸O-water. The incorporation of the ¹⁸O-labeling into the reducing end of N-glycans is simply and efficiently achieved during peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidase F release. This process provides a 2-Da mass difference compared with the N-glycans released in ¹⁶O-water. A mathematical calculation method was also developed to determine the ¹⁸O/¹⁶O ratios from isotopic peaks. Application of this method to several standard glycoprotein mixtures and human serum demonstrated that this method can facilitate the relative quantitation of N-glycans over a linear dynamic range of two orders, with high accuracy and reproducibility.     

Optimization of Data-Dependent Acquisition Parameters for Coupling High-Speed Separations with LC-MS/MS for Protein Identifications

Recent developments in chromatography, such as ultra-HPLC and superficially porous particles, offer significantly improved peptide separation. The narrow peak widths, often only several seconds, can permit a 15-min liquid chromatography run to have a similar peak capacity as a 60-min run using traditional HPLC approaches. In theory, these larger peak capacities should provide higher protein coverage and/or more protein identifications when incorporated into a proteomic workflow. We initially observed a decrease in protein coverage when implementing these faster chromatographic approaches, due to data-dependent acquisition (DDA) settings that were not properly set to match the narrow peak widths resulting from newly implemented, fast separation techniques. Oversampling of high-intensity peptides lead to low protein-sequence coverage, and tandem mass spectra (MS/MS) from lower-intensity peptides were of poor quality, as automated MS/MS events were occurring late on chromatographic peaks. These observations led us to optimize DDA settings to use these fast separations. Optimized DDA settings were applied to the analysis of Trypanosome brucei peptides, yielding peptide identifications at a rate almost five times faster than previously used methodologies. The described approach significantly improves protein identification workflows that use typical available instrumentation.     

The Use of Ammonium Formate as a Mobile-Phase Modifier for LC-MS/MS Analysis of Tryptic Digests

A major challenge facing current mass spectrometry (MS)-based proteomics research is the large concentration range displayed in biological systems, which far exceeds the dynamic range of commonly available mass spectrometers. One approach to overcome this limitation is to improve online reversed-phase liquid chromatography (RP-LC) separation methodologies. LC mobile-phase modifiers are used to improve peak shape and increase sample load tolerance. Trifluoroacetic acid (TFA) is a commonly used mobile-phase modifier, as it produces peptide separations that are far superior to other additives. However, TFA leads to signal suppression when incorporated with electrospray ionization (ESI), and thus, other modifiers, such as formic acid (FA), are used for LC-MS applications. FA exhibits significantly less signal suppression, but is not as effective of a modifier as TFA. An alternative mobile-phase modifier is the combination of FA and ammonium formate (AF), which has been shown to improve peptide separations. The ESI-MS compatibility of this modifier has not been investigated, particularly for proteomic applications. This work compares the separation metrics of mobile phases modified with FA and FA/AF and explores the use of FA/AF for the LC-MS analysis of tryptic digests. Standard tryptic-digest peptides were used for comparative analysis of peak capacity and sample load tolerance. The compatibility of FA/AF in proteomic applications was examined with the analysis of soluble proteins from canine prostate carcinoma tissue. Overall, the use of FA/AF improved online RP-LC separations and led to significant increases in peptide identifications with improved protein sequence coverage.     

“De novo” sequencing of peptides recovered from in-gel digested proteins by nanoelectrospray tandem mass spectrometry

Proteins separated by one-dimensional or two-dimensional gel electrophoresis can be digested in-gel with trypsin and the recovered peptides can be sequenced de novo using triple quadrupole or hybrid quadrupole time-of-flight instruments equipped with a nanoelectrospray ion source. The peptide sequences determined provide useful information for identification of proteins by homology searching for cloning of the cognate genes by PCR based approaches.     

Identification of neuropeptide FF-related peptides in human cerebrospinal fluid by mass spectrometry

Several neuropeptide FF (NPFF)-related peptides, known as modulators of the opioid system, have been previously characterized in bovine and rodent brain. Reverse-phase high pressure liquid chromatography (HPLC) fractions of a human with normal pressure hydrocephalus cerebrospinal fluid (CSF), co-migrating with NPFF-related synthetic peptides, were characterized by capillary HPLC coupled on-line to nanospray ion trap tandem mass spectrometry. Two peptides present in the pro-NPFF(A) precursor, NPAF (AGEGLNSQFWSLAAPQRF-NH2) and NPSF (SLAAPQRF-NH2), were identified. The monitoring of NPFF-related peptides in human CSF can be helpful to understand their roles in pain sensitivity.     

5-Methyltetrahydrofolic acid and folic acid measured in plasma with liquid chromatography tandem mass spectrometry: applications to folate absorption and metabolism

We describe a liquid chromatography (LC) tandem mass spectrometry (MS-MS) method for the determination of 5-methyltetrahydrofolic acid (5-methylTHF) and folic acid concentrations and enrichments in human plasma. It was used to study absorption and initial metabolism in five volunteers with two simultaneously administered oral test doses ([(13)C(6)]folic acid in capsules and [(2)H(2)]folic acid in a drink). [(13)C(5)]5-methylTHF and [(2)H(4)]folic acid were used as internal standards. Plasma samples (2 ml) were purified using folate binding protein affinity columns, followed by a concentration step. After LC separation, folates were detected using positive electrospray ionization MS-MS under multiple reaction monitoring conditions. Calibrations were linear for 5-methylTHF over the range 1.2 x 10(-11) (=limit of detection) to 3.2 x 10(-7)mol/L and for folic acid over the range 5 x 10(-10) (=limit of detection) to 4.5 x 10(-8)mol/L. For 5-methylTHF concentration in plasma, intraassay coefficient of variation was within 8.6% (and for unlabeled 5-methylTHF it was within 2.8%) and interassay coefficient of variation was within 9.0%. For folic acid concentrations these coefficient of variations were within 7.5% and within 6.5%, respectively. The [(13)C(6)] and [(2)H(2)] isotopomers of folic acid and 5-methylTHF were measured in the plasma of each volunteer for 8h. After accounting for the time delay due to capsule opening, the modeling results showed no significant differences in absorption time, first pass effect, and elimination rate in the folic acid test doses in capsule or drink. We conclude that LC-MS-MS offers increased sensitivity for quantification of plasma concentrations and enrichments of 5-methylTHF and folic acid and is applicable to stable-isotope studies in humans.     

Quantification of seminolipid by LC-ESI-MS/MS-multiple reaction monitoring: compensatory levels in Cgt mice

Seminolipid, also known as sulfogalactosylglycerolipid (SGG), plays important roles in male reproduction. Therefore, an accurate and sensitive method for SGG quantification in testes and sperm is needed. Here we compare SGG quantitation by the traditional colorimetric Azure A assay with LC-ESI-MS/MS using multiple reaction monitoring (MRM). Inclusion of deuterated SGG as the internal standard endowed accuracy to the MRM method. The results showed reasonable agreement between the two procedures for purified samples, but for crude lipid extracts, the colorimetric assay significantly overestimated the SGG content. Using ESI-MS/MS MRM, C16:0-alkyl/C16:0-acyl SGG of Cgt^+/− mice was quantified to be 406.06 ± 23.63 μg/g testis and 0.13 ± 0.02 μg/million sperm, corresponding to 78% and 87% of the wild-type values, respectively. CGT (ceramide galactosyltransferase) is a critical enzyme in the SGG biosynthesis pathway. Cgt^−/− males depleted of SGG are infertile due to spermatogenesis arrest. However, Cgt^+/− males sire offspring. The higher than 50% expression level of SGG in Cgt^+/− animals, compared with the wild-type expression, might be partly due to compensatory translation of the active CGT enzyme. The results also indicated that 78% of SGG levels in Cgt^+/− mice were sufficient for normal spermatogenesis.     

The Nucleotide‐Dependent Interactome of Rice Heterotrimeric G‐Protein α ‐Subunit

The rice heterotrimeric G‐protein complex, a guanine‐nucleotide‐dependent on‐off switch, mediates vital cellular processes and responses to biotic and abiotic stress. Exchange of bound GDP (resting state) for GTP (active state) is spontaneous in plants including rice and thus there is no need for promoting guanine nucleotide exchange in vivo as a mechanism for regulating the active state of signaling as it is well known for animal G signaling. As such, a master regulator controlling the G‐protein activation state is unknown in plants. Therefore, an ab initio approach is taken to discover candidate regulators. The rice Gα subunit (RGA1) is used as bait to screen for nucleotide‐dependent protein partners. A total of 264 proteins are identified by tandem mass spectrometry of which 32 were specific to the GDP‐bound inactive state and 22 specific to the transition state. Approximately, 10% are validated as previously identified G‐protein interactors.     

Simultaneous determination of type A-& B-trichothecenes and zearalenone in cereals by High Performance Liquid Chromatography — Tandem Mass Spectrometry

A rapid quantitative method for the simultaneous determination of the majorFusarium mycotoxins nivalenol, deoxynivalenol, fusarenon-X, 3-acetyl-deoxynivalenol, 15-acetyl-deoxynivalenol, diacetoxyscirpenol, HT-2 toxin, T-2 toxin and zearalenone in maize and wheat was developed. Raw extracts (acetonitrile/water 84/16) are cleaned-up with MycoSep^® columns., Chromatographic separation and end determination is carried out by HPLC-APCI-MS/MS.HPLC run times of 10 minutes considerably increases sample throughput and make this method suitable for routine analysis. The use of a triple quadrupole mass spectrometer allows the selective detection of the mycotoxins and their quantification in the low μg/kg-range.     

Whole-Cell Protein Identification Using the Concept of Unique Peptides

A concept of unique peptides(CUP)was proposed and implemented to identify whole-cell proteins from tandem mass spectrometry(MS/MS)ion spectra.A unique peptide is defined as a peptide,irrespective of its length,that exists only in one protein of a proteome of interest,despite the fact that this peptide may appear more than once in the same protein.Integrating CUP,a two-step whole-cell protein identification strategy was developed to further increase the confidence of identified proteins.A dataset containing 40,243 MS/MS ion spectra of Saccharomyces cerevisiae and protein identification tools including Mascot and SEQUEST were used to illustrate the proposed concept and strategy.Without implementing CUP,the proteins identified by SEQUEST are 2.26 fold of those identified by Mascot.When CUP was applied,the proteins bearing unique peptides identified by SEQUEST are3.89 fold of those identified by Mascot.By cross-comparing two sets of identified proteins,only 89 common proteins derived from CUP were found.The key discrepancy between identified proteins was resulted from the filtering criteria employed by each protein identification tool.According to the origin of peptides classified by CUP and the commonality of proteins recognized by protein identification tools,all identified proteins were cross-compared,resulting in four groups of proteins possessing different levels of assigned confidence.     

Approaches to labeling and identification of active site residues in glycosidases.

Glycosidases play a key role in a number of biological processes and, as such, are of considerable clinical and biotechnological importance. Knowledge of the identifies of catalytically important active site residues is essential for understanding the catalytic mechanism, for enzyme classification, and for targeted bioengineering of glycosidases with altered characteristics. Here we review and discuss traditional strategies and novel approaches based on tandem mass spectrometry for the identification of the key active site residues in glycosidases.     

Tandem mass spectrometric assay for the determination of carnitine palmitoyltransferase II activity in muscle tissue

Carnitine palmitoyltransferase II (CPT-II) mediates the import of long-chain fatty acids into the mitochondrial matrix for subsequent beta-oxidation. Defects of CPT-II manifest as a severe neonatal hepatocardiomuscular form or as a mild muscular phenotype in early infancy or adolescence. CPT-II deficiency is diagnosed by the determination of enzyme activity in tissues involving the time-dependent conversion of radiolabeled CPT-II substrates (isotope-exchange assays) or the formation of chromogenic reaction products. We have established a mass spectrometric assay (MS/MS) for the determination of CPT-II activity based on the stoichiometric formation of acetylcarnitine in a coupled reaction system. In this single-tube reaction system palmitoylcarnitine is converted by CPT-II to free carnitine, which is subsequently esterified to acetylcarnitine by carnitine acetyltransferase. The formation of acetylcarnitine directly correlates with the CPT-II activity. Comparison of the MS/MS method (y) with our routine spectrophotometric assay (x) revealed a linear regression of y = 0.58x + 0.12 (r = 0.8369). Both assays allow one to unambiguously detect patients with the muscular form of CPT-II deficiency. However, the higher specificity and sensitivity as well as the avoidance of the drawbacks inherent in the use of radiolabeled substrates make this mass spectrometric method most suitable for the determination of CPT-II activity.     

Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA

Protein-nucleic acid complexes are commonly studied by photochemical cross-linking. UV-induced cross-linking of protein to nucleic acid may be followed by structural analysis of the conjugated protein to localize the cross-linked amino acids and thereby identify the nucleic acid binding site. Mass spectrometry is becoming increasingly popular for characterization of purified peptide-nucleic acid heteroconjugates derived from UV cross-linked protein-nucleic acid complexes. The efficiency of mass spectrometry-based methods is, however, hampered by the contrasting physico-chemical properties of nucleic acid and peptide entities present in such heteroconjugates. Sample preparation of the peptide-nucleic acid heteroconjugates is, therefore, a crucial step in any mass spectrometry-based analytical procedure. This study demonstrates the performance of four different MS-based strategies to characterize E. coli single-stranded DNA binding protein (SSB) that was UV-cross-linked to a 5-iodouracil containing DNA oligomer. Two methods were optimized to circumvent the need for standard liquid chromatography and gel electrophoresis, thereby dramatically increasing the overall sensitivity of the analysis. Enzymatic degradation of protein and oligonucleotide was combined with miniaturized sample preparation methods for enrichment and desalting of cross-linked peptide-nucleic acid heteroconjugates from complex mixtures prior to mass spectrometric analysis. Detailed characterization of the peptidic component of two different peptide-DNA heteroconjugates was accomplished by matrix-assisted laser desorption/ionization mass spectrometry and allowed assignment of tryptophan-54 and tryptophan-88 as candidate cross-linked residues. Sequencing of those peptide-DNA heteroconjugates by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry identified tryptophan-54 and tryptophan-88 as the sites of cross-linking. Although the UV-cross-linking yield of the protein-DNA complex did not exceed 15%, less than 100 pmole of SSB protein was required for detailed structural analysis by mass spectrometry.     

电喷雾串联质谱图的叠合与多肽序列分析

利用离子阱电喷雾串联质谱仪,在选择性改变某些食品参数的条件下对模式分子Met-脑啡肽和自行固相化学合成的7肽及其修饰产物、10肽和20肽进行碎裂处理,从而获得一系列具有一定差异的串联质谱图。选择具有适当互补性的图谱进行叠合处理,得到具有连贯性“三联套”（triplet）及“二联套”（doublet）碎片离子峰的叠合串联质谱图,据此可以方便准确地角析出多肽的氨基酸序列。实验结果表明,这种方法在多肽的质谱法测定中具有一定的实用性。     

Quantitation of cardiolipin molecular species in spontaneously hypertensive heart failure rats using electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry has previously been used to probe qualitative changes in the phospholipid cardiolipin (CL), but it has rarely been used in a quantitative manner. We assessed changes in the amount of individual molecular species of cardiac CL present in a model of congestive heart failure using 1,1',2,2'-tetramyristoyl cardiolipin as an internal standard. There was a linear relationship between the ratio of the negative molecular ion ([M-H]-) current from four different CL reference standards and the [M-H]- from the internal standard, as a function of the concentration of CL molecular species. Therefore, this internal standard can be used to quantitate many naturally occurring CL molecular species over a wide range of CL concentrations. Using this method, changes to individual molecular species of CL in failing hearts from male spontaneously hypertensive heart failure rats were examined. CL isolated from cardiac mitochondria was compared with left ventricular tissue to demonstrate the feasibility of extracting and quantitating CL from either mitochondrial or tissue samples. The acyl chain composition of individual CL molecular species was identified using tandem mass spectrometry. In animals with heart failure, the major cardiac CL species (tetralinoloyl) decreased significantly, whereas other minor CL species were significantly increased.     

Computing positional isotopomer distributions from tandem mass spectrometric data

The isotopomer distributions of metabolites are invaluable pieces of information in the computation of the flux distribution in a metabolic network. We describe the use of tandem mass spectrometry with the daughter ion scanning technique in the discovery of positional isotopomer distributions (PID). This technique increases the possibilities of mass spectrometry since given the same fragment ions, it uncovers more information than the full scanning mode. The mathematics of the new technique is slightly more complicated than the techniques needed by full scanning mode methods. Our experiments, however, show that in practice the inadequacy of the fragmentation of amino acids in the tandem mass spectrometer does not allow uncovering the PID exactly even if the daughter ion scanning is used. The computational techniques have been implemented in a MATLAB application called PIDC (Positional Isotopomer Distribution Calculator).     

Electrospray mass spectrometry of human hair wax esters

Wax esters extracted from human hair have been examined by capillary GC-MS and by nano electrospray ionization (ESI) mass spectrometry using a tandem quadrupole mass spectrometer. Initially, the wax esters were examined by capillary GC-MS using conventional means, thus revealing an incomplete chromatographic resolution of the complex array of >200 wax esters ranging from 28 to 40 carbons in length, including saturated/straight-chained, unsaturated/straight-chained, saturated/branched, and unsaturated/branched molecular species. ESI of wax esters produced ammonium adduct ions [M+NH4]+, and collisional activation of these ions formed abundant [RCO2H2]+ product ions. Wax esters containing a double bond in the fatty acyl or fatty alcohol portion of the molecule revealed identical behavior, suggesting little influence of the double bond on the ionization process or subsequent decomposition. The wax ester mixture was analyzed by ESI and tandem mass spectrometry using multiple reaction monitoring and neutral loss scanning. The neutral loss experiment [loss of NH3 and CH2=CH-(CH2)nCH3] was particularly effective at rapidly surveying the complex biological mixture, identifying>160 different wax esters that range from 24 to 42 total carbons.     

基于质谱和生物信息学分析的小菜蛾蛋白质鉴定

本研究以非模式昆虫小菜蛾Plutella xylostella为材料, 对比2, 3, 4龄幼虫的蛋白质组双向电泳图谱, 得到24个蛋白质差异点, 从中选取了编号为1111的差异表达蛋白质点进行质谱鉴定和生物信息学分析. 采用胶内酶解的多肽进行MALDI-TOF/TOF分析, 获得该点的肽质量指纹图谱（PMF）及串联质谱（MS/MS）图谱。将获得的PMF分别用MASCOT和ProFound等常用软件在NCBInr的Metazoa蛋白质数据库进行搜索, 匹配结果不理想. 进一步用PMF+MS/MS谱图搜索NCBInr的Metazoa蛋白质数据库, 以及小菜蛾EST数据库。 在NCBInr库中匹配结果为拟暗果蝇Drosophila pseudoobscura中的一种假定蛋白GA18218-PA, 而用EST库搜索的结果为家蚕Bombyx mori的ATP合酶的亚基。为验证搜索结果, 将该蛋白质点进行磺基异硫氰酸苯酯（SPITC）化学衍生后de novo测序, 最后确认该点可能为ATP合酶的一个亚基。最后着重讨论了蛋白质的质谱鉴定与生物信息学分析的联合使用, 希望据此选择出最适合于非模式昆虫蛋白质组学鉴定的方法。