反相高效液相色谱法测定蟾酥中的3种蟾毒内酯

建立了一种基于毛细管反相液相色谱-串联质谱联用技术和质谱峰强度数据处理的肽段鉴定和相对定量分析方法。该方法无需对样品中的肽进行化学标记,在对样品进行反相色谱分离和串联质谱分析后,将二级质谱扫描数据进行蛋白质数据库搜索,获得所鉴定肽段的序列、保留时间、质荷比、带电荷数等定性信息;再以此为定位依据,在全扫描质谱数据中提取该肽段对应的离子峰并以该离子峰的峰强度作为定量信息,从而实现对不同样品中的共有肽段进行差异比较分析。以标准蛋白酶解混合肽段为实验对象,以肽段相对强度的相对标准偏差为指标,考察了该方法用于肽段相对定量分析的重现性、检测动态范围以及浓度标准曲线等,为将该方法用于生物样品中内源性肽的差异分析奠定了基础。。     

基于保留时间和质荷比匹配的液相色谱-质谱联用技术用于非标记肽段的差异分析

建立了一种无需化学标记的,基于纳升级毛细管液相色谱-电喷雾离子阱质谱联用技术和质谱数据处理的肽段差异分析方法。本方法采用定量差异分析与肽序列鉴定分析分别进行的策略,首先对样品进行质谱全扫描的液质全谱式分析,在全扫描质谱数据中提取肽特征点信息,通过保留时间和质荷比参数匹配不同样品中的共有肽特征点,比较其相对峰强度有无差异。最后对样品中存在丰度差异的肽特征点进行选择性二级质谱分析和序列鉴定,从而实现复杂样品中肽段的差异比较分析。以血浆蛋白酶解混合物为实验对象,考察了本方法用于肽段相对定量分析的重现性以及浓度信号响应曲线等。结果表明:提取的肽特征点峰强度相对标准偏差的中值<22%,肽段离子强度动态范围达3个数量级,在5～1000fmol范围内对肽段定量具有良好线性关系。本方法可用于不同条件样品中具有倍数差异的内源性肽的比较分析。     

基于在线二维色谱的不同生长时期鹿茸的比较蛋白质组分析

建立了基于在线二维弱阴离子交换色谱-反相液相色谱(2D-WAX-RPLC)的蛋白质分离系统,并用于不同生长时期鹿茸的比较蛋白质组分析。以5种标准蛋白质的混合物为样品,考察了系统的重现性。通过改变标准蛋白质之间的浓度比,研究了该系统进行蛋白质相对定量的能力。在此基础上,针对4个不同生长时期的鹿茸样品,分别采用5种不同的方法进行蛋白质提取,经2D-WAX-RPLC分离后,收集各生长时期对应蛋白质的峰高最大比超过2的组分。酶解后,采用微柱反相液相色谱-串联质谱(μRPLC-MS/MS)进行肽段的分离鉴定;共从9个差异蛋白质峰中鉴定到了22个差异蛋白质。研究结果表明,利用基于蛋白质水平的在线二维液相色谱分离技术找寻差异蛋白质,具有重现性好、自动化程度高等优点,可用于开展比较蛋白质组学的研究。     

串联飞行时间质谱中亚胺离子的断裂特征及其在肽段鉴定中的作用

基质辅助激光解吸电离-串联飞行时间质谱(MALDI-TOF/TOF)产生的亚胺离子可以提供丰富的肽段组成信息,该方法通常用于基于数据库搜索的蛋白质鉴定,或者结合化学衍生法用于从头测序,因而在一定程度上限制了对亚胺离子的认识及应用。本研究利用239个串联质谱探索MALDI-TOF/TOF中亚胺离子的断裂特征以及它们在肽段鉴定中的应用,发现在高能碰撞诱导解离条件下组氨酸等14种氨基酸可产生较强的亚胺离子信号(>50%阳性率),氨基酸的化学结构、位置效应和氨基酸残基个数是影响碎片离子强度的主要因素。此外,探讨了亚胺离子应用过程中的假阳性问题,提出亚胺离子相对强度的比较可以降低假阳性和提高肽段鉴定确定度,有助于完善目前的数据库搜索算法和辅助从头测序分析。     

亲水作用-反相二维液相色谱串联质谱法鉴定水稻蛋白质

建立了亲水作用-反相二维液相色谱串联质谱分析水稻叶片蛋白质组学的方法。利用标准肽段系统分析了液相色谱流动相酸碱度对二维亲水作用-反相色谱系统正交性的影响。结果表明,第一维亲水作用色谱在碱性(pH 9.3)和第二维反相色谱在酸性(pH 3.3)的条件下,正交性最佳(R~2=0.34113)。在此基础上,结合馏分收集技术进一步评价了本测试系统在水稻叶片蛋白质分析中的正交性。结果表明,在所有馏分收集组分中,鉴定次数小于2次的水稻叶片肽段占总肽段数目的 50%以上,且一维液相色谱馏分收集的肽段在第二维色谱及质谱分离分析中,可以较好地分布在不同时间段的洗脱窗口,表明本研究建立的亲水作用-反相二维液相色谱串联质谱结合馏分收集技术在复杂水稻叶片蛋白质分离鉴定中可提供良好的的分离正交性。结合水稻蛋白质数据库检索,共鉴定出207345个肽段,归属于2930个蛋白质簇。     

反相高效液相色谱双梯度洗脱分离肽混合物及质谱分析

复杂肽段混合物的有效分离是高覆盖率地鉴定蛋白质混合物的前提。“鸟枪法”(Shotgun)蛋白质组学研究策略通常采用蛋白酶切、二维液相色谱-串联质谱分析肽段混合物从而鉴定蛋白质,其中高效率地分离肽段混合物是关键步骤之一。本文通过pH梯度结合有机溶剂梯度的反相高效液相色谱(RP-HPLC)进行一维液相色谱分离,按等时间间隔收集馏分并将一个梯度的前段的一个馏分与后段一个馏分混合,然后进行纳升级液相色谱-质谱联用(nanoRPLC-MS/MS)分析。将该方法应用于酵母蛋白质的分离和鉴定,实验结果为: 与常规的强阳离子色谱-反相液相色谱-质谱分离鉴定方法相比,采用pH梯度结合有机相梯度的RP-HPLC-RPLC-MS分离鉴定方法多鉴定到567个酵母蛋白质(簇,含有3035个唯一肽段);其中鉴定到肽段的pI分布范围为3.42～12.01,相对分子质量范围为587.67～3499.79;蛋白质的pI分布范围为3.82～12.19,相对分子质量范围为3446.55～432905。该结果表明这种方法在复杂体系蛋白质组分离鉴定中具有明显的优势,在蛋白质组学研究中有较好的应用前景。     

高效液相色谱-串联质谱法同时测定夏天无中的4种生物碱

建立了高效液相色谱-电喷雾串联四极杆质谱同时测定夏天无中4种生物碱的分析方法。夏天无样品用甲醇超声提取,提取溶液过滤并用甲醇稀释后分析。色谱分离采用C18反相色谱柱(150 mm×2.1 mm, 3.5 μm),流动相为0.2%乙酸水溶液和乙腈,梯度洗脱。电喷雾串联质谱在多反应监测(MRM)模式下检测目标分析物,以保留时间和特征离子对(母离子和两个碎片离子)信息比较进行定性分析和定量分析。4种生物碱的检出限(LOD)为0.02～0.2 μg/L,定量限(LOQ)为0.07～0.66 μg/L,加标回收率为93.6%～103.5%,相对标准偏差小于3.8%。该方法简便、准确、灵敏,可用于夏天无中药材的质量控制。     

比较纳升反相色谱-串联质谱与毛细管区带电泳-串联质谱用于自顶向下蛋白质组学

自顶向下蛋白质组学的一个重要难题是缺乏与质谱可以在线连用并且可以提供高效蛋白质分离的液相分离技术。毛细管区带电泳与纳升反相色谱都可以与质谱在线连用,并且在复杂蛋白质样品分析方面也都有了显著的提升。在这里,我们首次比较了先进的纳升反相色谱-串联质谱与毛细管区带电泳-串联质谱平台用于自顶向下蛋白质组学分析。相对于纳升反相色谱-质谱而言,毛细管区带电泳-质谱可以将标准蛋白质样品的消耗量降低10倍,而且保持与纳升反相色谱-质谱相当的蛋白质信号强度。有意思的是,与毛细管区带电泳-质谱相比,纳升反相色谱-质谱可以获得更高的蛋白质分子的气相价态。这个现象可能是由于反相流动相中的高浓度乙腈使得蛋白质变性的更加充分。从1微克的大肠杆菌蛋白质样品中,毛细管区带电泳-串联质谱可以鉴定到159个蛋白质和513个蛋白质变体,而纳升反相色谱-串联质谱仅鉴定到105个蛋白质和277个蛋白质变体。当将大肠杆菌蛋白质的上样量提高到8微克时,纳升反相色谱-串联质谱可以鉴定到245个蛋白质和1004个蛋白质变体。由于纳升反相色谱-串联质谱具有比毛细管区带电泳-串联质谱更高的上样量与更宽的分离窗口,当蛋白质样品量不受限制时,纳升反相色谱-串联质谱具有明显的优势。但是,在痕量样品分析方面,毛细管区带电泳-串联质谱具有更大的潜力。     

高分辨飞行时间质谱在蛋白质组学相对定量分析中的应用

利用TripleTOF 5600高分辨质谱仪分析牛血清白蛋白等3种蛋白质标准品,研究了质谱离子强度与蛋白质样品相对含量的相关性。蛋白质标准品用胰酶酶切后,稀释成1~1024 fmol/7μL的系列溶液,考察在1~1024 fmol 上样量情况下,肽段的前体离子计数( cps)、蛋白质全部肽段的离子计数之和以及被检出肽段数目与上样量的相关性,以及相同样品在3次平行实验之间这些数值的变化幅度。结果表明。被检出肽段数目与上样量正相关,当cps超过1000时,所有肽段离子强度之和与上样量呈线性关系,但是用最灵敏肽段的离子强度表示更为准确。3次测量同一肽段的最高离子强度通常不会超过最低强度的1.5倍,提示当不同样品中同一蛋白的离子强度相差3倍以上是判断不同样品中相同蛋白质的含量具有差异的可靠阈值。本研究提供了一种利用高分辨率和高扫描速度蛋白质组组学定性数据进行半定量分析的方法,简便、快速,可为相关生物学和医学研究提供参考。     

高效液相色谱-串联质谱法检测乳制品中10种氨基糖苷类抗生素残留

建立了乳制品中链霉素、双氢链霉素、新霉素、卡那霉素、妥布霉素、庆大霉素、安普霉素、潮霉素B、巴龙霉素、阿米卡星等10种氨基糖苷类抗生素(aminoglycosides, AGs)残留的高效液相色谱-串联质谱(HPLC-MS/MS)检测方法。乳制品提取液经亲水-亲脂平衡(hydrophilic- lipophilic balance, HLB)柱净化后,采用反相离子对高效液相色谱分离,电喷雾串联四极杆质谱检测。对样品前处理条件、液相色谱流动相以及质谱条件进行了优化。结果表明: 10种AGs在20～1000 μg/L范围内定量离子的峰面积和样品的质量浓度之间有很好的线性关系;在乳制品中的加标回收率为71.2%～101.7%,相对标准偏差为3.4%～13.8%。该方法简便、灵敏、准确,可用于乳制品中多种AGs残留的同时检测。     

Microwave-assisted acid hydrolysis of proteins combined with liquid chromatography MALDI MS/MS for protein identification

Simple and efficient digestion of proteins, particularly hydrophobic membrane proteins, is of significance for comprehensive proteome analysis using the bottom-up approach. We report a microwave-assisted acid hydrolysis (MAAH) method for rapid protein degradation for peptide mass mapping and tandem mass spectrometric analysis of peptides for protein identification. It uses 25% trifluoroacetic acid (TFA) aqueous solution to dissolve or suspend proteins, followed by microwave irradiation for 10 min. This detergent-free method generates peptide mixtures that can be directly analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) without the need of extensive sample cleanup. LC-MALDI MS/MS analysis of the hydrolysate from 5 microg of a model transmembrane protein, bacteriorhodopsin, resulted in almost complete sequence coverage by the peptides detected, including the identification of two posttranslational modification sites. Cleavage of peptide bonds inside all seven transmembrane domains took place, generating peptides of sizes amenable to MS/MS to determine possible sequence errors or modifications within these domains. Cleavage specificity, such as glycine residue cleavage, was observed. Terminal peptides were found to be present in relatively high abundance in the hydrolysate, particularly when low concentrations of proteins were used for MAAH. It was shown that these peptides could still be detected from MAAH of bacteriorhodopsin at a protein concentration of 1 ng/microl or 37 fmol/microl. To evaluate the general applicability of this method, it was applied to identify proteins from a membrane protein enriched fraction of cell lysates of human breast cancer cell line MCF7. With one-dimensional LC-MALDI MS/MS, a total of 119 proteins, including 41 membrane-associated or membrane proteins containing one to 12 transmembrane domains, were identified by MS/MS database searching based on matches of at least two peptides to a protein.     

Automated neutral loss and data dependent energy resolved "pseudo MS3" for the targeted identification, characterization and quantitative analysis of methionine- containing peptides

A strategy involving the fixed-charge sulfonium ion derivatization, stable isotope labeling, capillary high- performance liquid chromatography and automated data dependent neutral loss scan mode tandem mass spectrometry (MS/MS) and "pseudo multiple mass spectrometry (MS(3))" product ion scans in a triple quadrupole mass spectrometer has been developed for the "targeted" gas-phase identification, characterization and quantitative analysis of low abundance methionine-containing peptides present within complex protein digests. Selective gas-phase "enrichment" and identification is performed via neutral loss scan mode MS/MS, by low energy collision-induced dissociation of the derivatized methionine side chain, resulting in the formation of a single characteristic product ion. Structural characterization of identified peptides is then achieved by automatically subjecting the characteristic neutral loss product ion to further dissociation by data dependent product ion scan mode pseudo MS(3) under higher collision energy conditions. Quantitative analysis is achieved by measurement of the abundances of characteristic product ions formed by sequential neutral loss scan mode MS/MS experiments from "light" ((12)C) and "heavy" ((13)C) stable isotope encoded fixed-charge derivatized peptides. In contrast to MS-based quantitative analysis strategies, the neutral loss scan mode MS/MS method employed here was able to achieve accurate quantification for individual peptides at levels as low as 100 fmol and at abundance ratios ranging from 0.1 to 10, present within a complex protein digest.     

HPTLC/DESI-MS imaging of tryptic protein digests separated in two dimensions

Desorption electrospray ionization mass spectrometry (DESI-MS) was demonstrated as a method to detect and identify peptides from two-dimensional separations of cytochrome c and myoglobin tryptic digests on ProteoChrom HPTLC Cellulose sheets. Data-dependent tandem mass spectra were acquired during lane scans across the TLC plates. Peptides and the corresponding proteins were identified using a protein database search software. Two-dimensional distributions of identified peptides were mapped for each separated protein digest. Sequence coverages for cytochrome c and myoglobin were 81 and 74%, respectively. These compared well with those determined using the more standard HPLC/ESI-MS/MS approach (89 and 84%, respectively). Preliminary results show that use of more sensitive instrumentation has the potential for improved detection of peptides with low R(f) values and improvement in sequence coverage. However, less multiple charging and more sodiation were seen in HPTLC/DESI-MS spectra relative to HPLC/ESI-MS spectra, which can affect peptide identification by MS/MS. Methods to increase multiple charging and reduce the extent of sodiation are currently under investigation.     

Identification of microbial mixtures by LC-selective proteotypic-peptide analysis (SPA)

This paper describes a method--using a combination of LC-MS/MS of selected bacteria-specific peptides and database search--for determining the species of bacteria present in a mixture. We identified the proteotypic peptides that were associated with specific bacteria by searching protein databases for the LC-MS/MS data. The retention time windows for specific peptide markers were used as an extra constraint so that the peptide markers of many bacterial species could be analyzed in a single LC-selective proteotypic-peptide analysis (SPA). We performed LC-MS/MS analyses on the proteolytic digest of cell extracts and monitored only the selected marker peptide ions at given elution time windows. The corresponding bacterial species could be characterized when the selected peptides that eluted at expected elution windows were identified correctly from the database. We managed to identify up to eight bacterial species simultaneously during a single LC-MS/MS analysis, as well as bacteria mixed in various abundances. Two marker ions having similar values of m/z, but obtained from two different bacterial samples, which would otherwise be selected as precursors within mass tolerance and would complicate the MS/MS data, were time-resolved using LC and then used to correctly identify their bacterial sources. The coupling of selective MS/MS monitoring with separation methods, such as LC, provides a highly selective and accurate analytical method for characterizing complex mixtures of bacterial species.     

Atmospheric pressure laser desorption/ionization on porous silicon

A recently developed commercial atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) source (MassTech, Inc.) was modified to adopt commercially available DIOS plates (Mass Consortium Corp.) for the studies of laser desorption from the surface of porous silicon under atmospheric pressure conditions. The feasibility of atmospheric pressure laser desorption/ionization from the surface of porous silicon (AP-DIOS) was demonstrated. The advantages of this new AP-DIOS technique include reasonably good sensitivity (subpicomole range for standard peptide mixtures), simplicity of sample preparation, uniformity of target spots and the absence of matrix peaks in the spectra. The AP-DIOS source was interfaced with a commercial ion trap (LCQ Classic, Thermo Finnigan) which additionally provides a unique MS(n) capability. The AP-DIOS spectrum of 250 fmol of unseparated tryptic digest of bovine serum albumin (BSA) was compared with that of AP-MALDI for the same compound. AP-DIOS offers significantly better coverage for the digest components in the mass range 200-1000 Da. The combined data of both techniques enabled us to nearly double the number of matched peaks in BSA digest analysis compared with AP-DIOS or AP-MALDI analysis separately.     

Tandem mass spectra of tryptic peptides at signal-to-background ratios approaching unity using electrospray ionization high-field asymmetric waveform ion mobility spectrometry/hybrid quadrupole time-of-flight mass spectrometry

High-field asymmetric waveform ion mobility spectrometry (FAIMS) has been coupled to a quadrupole time-of-flight mass spectrometer for the tandem mass spectrometric analysis of tryptic peptides of pig hemoglobin. Using FAIMS, low levels (fmol/microL) of multiply charged tryptic peptides were separated from relatively intense chemical background such that their tandem mass spectra (MS/MS) lacked many background-related fragment ions observed using a conventional ESI-QqTOFMS instrument. Substantial improvements in both first-order and tandem mass spectra were realized while maintaining approximately the same absolute intensities.     

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.     

Quantitative analysis of low‐abundance peptides in HeLa cell cytoplasm by targeted liquid chromatography/mass spectrometry and stable isotope dilution: emphasising the distinction between peptide detection and peptide identification

We present the application of a targeted liquid chromatography/mass spectrometry (LC/MS) approach developed on a linear ion trap for the evaluation of the abundance of cytoplasmic proteins from a HeLa cell extract. Using a standard data‐dependent approach, we identified some specific peptides from this extract which were also commercially available in their AQUA form (use for absolute quantitation). For some of the peptides, we observed a non‐linear response between the intensity and the added quantity which was then fitted using a quadratic fit. All AQUA peptides spiked into a mix of 3 µg of the HeLa cell digest extract were detected down to 16 fmol. We placed an emphasis on peptide detection which, in this study, is performed using a combination of properties such as three specific Q3‐like ion signatures (for a given Q1‐like selection) and co‐elution with the AQUA peptide counterparts. Detecting a peptide without necessarily identifying it using a search engine imposes less constraint in terms of tandem mass (MS/MS) spectra purity. An example is shown where a peptide is detected using those criteria but could not be identified by Mascot due to its lower abundance. To complement this observation, we used a cross‐correlation analysis approach in order to separate two populations of MS/MS fragments based on differences in their elution patterns. Such an approach opens the door to new strategies to analyse lower intensity peptide fragments. An in silico analysis of the human trypsinosome allows the evaluation of how unique are the sets of features that we are using for peptide detection. Copyright © 2010 John Wiley & Sons, Ltd.     

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.     

Plastic microchip liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometry using monolithic columns

A prototype array of monolithic liquid chromatography (LC) columns was prepared in a plastic microfluidic device for the off-line interface with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The microfluidic channels were fabricated on a cyclic olefin copolymer (COC) plate by hot embossing. An array of methacrylate monolithic columns was prepared in the microfluidic channels by UV-initiated polymerization. The deposition system employed a pulsed electric field to transfer the effluents from multiple columns directly onto MALDI targets with a non-contact deposition method reported by Ericson et al. [C. Ericson, Q.T. Phung, D.M. Horn, E.C. Peters, J.R. Fitchett, S.B. Ficarro, A.R. Salmon, L.M. Brill, A. Brock, Anal. Chem. 75 (2003) 2309]. To characterize the off-line interface of the multiple-channel microchip LC and the MALDI-MS for the analysis of peptide mixtures, the separation efficiency and reproducibility tests in each column were carried out by separating a peptide mixture from tryptic digested proteins and depositing the multiple effluents simultaneously on the MALDI target plate. Using a MALDI-TOF mass spectrometer with a mass accuracy of +/-1 Da for peptide assignments of digested bovine serum albumin (BSA), amino acid sequence coverage of around 59% was obtained for the microchip LC-MALDI-MS compared to 23% obtained by the MALDI-MS method without LC separation. In sensitivity tests for the detection of low abundance proteins in the presence of high concentration protein mixtures, as low as 10 fmol/mul (S/N = 10) of a spiked peptide in 1 microg of digested BSA could be detected. In the analysis of a mixture of three digested proteins (BSA, myoglobin, and cytochrome c), more than twice the amino acid sequence coverage was obtained for the microchip LC-MALDI-MS compared to MALDI-MS alone.