Quantification of the Dynamic Phosphorylation Process of ERK Using Stable Isotope Dilution Selective Reaction Monitoring Mass Spectrometry

Mitogen‐activated protein (MAP) kinase signaling is critical for various cellular responses, including cell proliferation, differentiation, and cell death. The MAP kinase cascade is conserved in the eukaryotic kingdom as a three‐tiered kinase module—MAP kinase kinase kinase, MAP kinase kinase, and MAP kinase—that transduces signals via sequential phosphorylation upon stimulation. Dual phosphorylation of MAP kinase on the conserved threonine‐glutamic acid‐tyrosine (TEY) motif is essential for its catalytic activity and signal activation; however, the molecular mechanism by which the two residues are phosphorylated remains elusive. In the present study, the pattern of dual phosphorylation of extracellular signal‐regulated kinase (ERK) is profiled on the TEY motif using stable isotope dilution (SID)‐selective reaction monitoring (SRM) mass spectrometry (MS) to elucidate the order and magnitude of endogenous ERK phosphorylation in cellular model systems. The SID‐SRM‐MS analysis of phosphopeptides demonstrates that tyrosine phosphorylation in the TEY motif is dynamic, while threonine phosphorylation is static. Analyses of the mono‐phosphorylatable mutants ERK^T202A and ERK^Y204F indicate that phosphorylation of tyrosine is not affected by the phosphorylation state of threonine, while threonine phosphorylation depends on tyrosine phosphorylation. The data suggest that dual phosphorylation of ERK is a highly ordered and restricted mechanism determined by tyrosine phosphorylation.     

Cellular Lipid Extraction for Targeted Stable Isotope Dilution Liquid Chromatography-Mass Spectrometry Analysis

The metabolism of fatty acids, such as arachidonic acid (AA) and linoleic acid (LA), results in the formation of oxidized bioactive lipids, including numerous stereoisomers^1,2. These metabolites can be formed from free or esterified fatty acids. Many of these oxidized metabolites have biological activity and have been implicated in various diseases including cardiovascular and neurodegenerative diseases, asthma, and cancer^3-7. Oxidized bioactive lipids can be formed enzymatically or by reactive oxygen species (ROS). Enzymes that metabolize fatty acids include cyclooxygenase (COX), lipoxygenase (LO), and cytochromes P450 (CYPs)^1,8. Enzymatic metabolism results in enantioselective formation whereas ROS oxidation results in the racemic formation of products.While this protocol focuses primarily on the analysis of AA- and some LA-derived bioactive metabolites; it could be easily applied to metabolites of other fatty acids. Bioactive lipids are extracted from cell lysate or media using liquid-liquid (l-l) extraction. At the beginning of the l-l extraction process, stable isotope internal standards are added to account for errors during sample preparation. Stable isotope dilution (SID) also accounts for any differences, such as ion suppression, that metabolites may experience during the mass spectrometry (MS) analysis⁹. After the extraction, derivatization with an electron capture (EC) reagent, pentafluorylbenzyl bromide (PFB) is employed to increase detection sensitivity^10,11. Multiple reaction monitoring (MRM) is used to increase the selectivity of the MS analysis. Before MS analysis, lipids are separated using chiral normal phase high performance liquid chromatography (HPLC). The HPLC conditions are optimized to separate the enantiomers and various stereoisomers of the monitored lipids¹². This specific LC-MS method monitors prostaglandins (PGs), isoprostanes (isoPs), hydroxyeicosatetraenoic acids (HETEs), hydroxyoctadecadienoic acids (HODEs), oxoeicosatetraenoic acids (oxoETEs) and oxooctadecadienoic acids (oxoODEs); however, the HPLC and MS parameters can be optimized to include any fatty acid metabolites¹³.Most of the currently available bioanalytical methods do not take into account the separate quantification of enantiomers. This is extremely important when trying to deduce whether or not the metabolites were formed enzymatically or by ROS. Additionally, the ratios of the enantiomers may provide evidence for a specific enzymatic pathway of formation. The use of SID allows for accurate quantification of metabolites and accounts for any sample loss during preparation as well as the differences experienced during ionization. Using the PFB electron capture reagent increases the sensitivity of detection by two orders of magnitude over conventional APCI methods. Overall, this method, SID-LC-EC-atmospheric pressure chemical ionization APCI-MRM/MS, is one of the most sensitive, selective, and accurate methods of quantification for bioactive lipids.     

Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry

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Highlights

• •Targeted mass spectrometry assay to quantify prion protein (PrP) in spinal fluid.
• •Precise measurement of PrP peptide concentration across protein domains.
• •Peptides are uniformly decreased in symptomatic prion disease patients.
• •Assay applicable to humans and preclinical species for drug development.

     

基于葡萄糖脉冲的同位素稀释质谱检测法标品制备

同位素稀释质谱检测法(IDMS)是目前进行胞内代谢物浓度高通量检测精度最高的一种方法,这个方法的关键就是制备待检测代谢物对应的~(13)C全标记的标品。传统制备~(13)C全标记标品的方法是采用批培养的模式获取,但该方法所制备的胞内代谢物浓度通常较低。通过以~(13)C全位标记葡萄糖作为唯一碳源培养毕赤酵母G/DSEL菌种,采用~(13)C全位标记葡萄糖脉冲刺激法,结合快速取样淬灭方法的新方法,成功制备了带~(13)C标记标品并提高了其浓度。经液质联用(LC-MS)与气质联用(GC-MS)结果分析,与传统制备方法相比,胞内大部分有机酸、磷酸糖、氨基酸和核苷酸类物质的浓度实现了约2–10倍的提高。因此底物脉冲法可以有效提高~(13)C全标葡萄糖的单位利用率,并能实现对胞内部分含量低于仪器检测限的代谢物的检测。     

Quantitation of 5-Methyltetrahydrofolic Acid in Dried Blood Spots and Dried Plasma Spots by Stable Isotope Dilution Assays

Because of minimal data available on folate analysis in dried matrix spots (DMSs), we combined the advantages of stable isotope dilution assays followed by LC-MS/MS analysis with DMS sampling to develop a reliable method for the quantitation of plasma 5-methyltetrahydrofolic acid in dried blood spots (DBSs) and dried plasma spots (DPSs) as well as for the quantitation of whole blood 5-methyltetrahydrofolic acid in DBSs. We focused on two diagnostically conclusive parameters exhibited by the plasma and whole blood 5-methyltetrahydrofolic acid levels that reflect both temporary and long-term folate status. The method is performed using the [²H₄]-labeled isotopologue of the vitamin as the internal standard, and three steps are required for the extraction procedure. Elution of the punched out matrix spots was performed using stabilization buffer including Triton X-100 in a standardized ultrasonication treatment followed by enzymatic digestion (whole blood only) and solid-phase extraction with SAX cartridges. This method is sensitive enough to quantify 27 nmol/L whole blood 5-methyltetrahydrofolic acid in DBSs and 6.3 and 4.4 nmol/L plasma 5-methyltetrahydrofolic acid in DBSs and DPSs, respectively. The unprecedented accurate quantification of plasma 5-methyltetrahydrofolic acid in DBSs was achieved by thermal treatment prior to ultrasonication, inhibiting plasma conjugase activity. Mass screenings are more feasible and easier to facilitate for this method in terms of sample collection and storage compared with conventional clinical sampling for the assessment of folate status.     

Identification and Quantification of Proteoforms by Mass Spectrometry

A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post‐translational modifications. In top‐down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top‐down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.     

Rapid and Precise Measurement of Serum Branched-Chain and Aromatic Amino Acids by Isotope Dilution Liquid Chromatography Tandem Mass Spectrometry

Background

Serum branched-chain and aromatic amino acids (BCAAs and AAAs) have emerged as predictors for the future development of diabetes and may aid in diabetes risk assessment. However, the current methods for the analysis of such amino acids in biological samples are time consuming.

Methods

An isotope dilution liquid chromatography tandem mass spectrometry (ID-LC/MS/MS) method for serum BCAAs and AAAs was developed. The serum was mixed with isotope-labeled BCAA and AAA internal standards and the amino acids were extracted with acetonitrile, followed by analysis using LC/MS/MS. The LC separation was performed on a reversed-phase C₁₈ column, and the MS/MS detection was performed via the positive electronic spray ionization in multiple reaction monitoring mode.

Results

Specific analysis of the amino acids was achieved within 2 min. Intra-run and total CVs for the amino acids were less than 2% and 4%, respectively, and the analytical recoveries ranged from 99.6 to 103.6%.

Conclusion

A rapid and precise method for the measurement of serum BCAAs and AAAs was developed and may serve as a quick tool for screening serum BCAAs and AAAs in studies assessing diabetes risk.     

Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues

The ability to accurately quantify proteins in formalin-fixed paraffin-embedded tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selectedreaction monitoring assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in formalin-fixed paraffin-embedded breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A multiplexed assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. Results showed a linear response over a calibration range of 0.012 to 100 fmol on column (R²: 0.99–1.00).The lower limit of quantification was 0.155 fmol on column for all peptides evaluated. The six HER2 peptides were quantified by selected reaction monitoring in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, which showed different levels of HER2 gene amplification as assessed by standard methods used in clinical pathology. The amounts of the six HER2 peptides were highly and significantly correlated with each other, indicating that peptide levels can be used as surrogates of protein amounts in formalin-fixed paraffin-embedded tissues. After normalization for sample size, selected reaction monitoring peptide measurements were able to correctly predict 90% of cases based on HER2 amplification as defined by the American Society of Clinical Oncology and College of American Pathologists. In conclusion, the developed assay showed good analytical performance and a high agreement with immunohistochemistry and fluorescence in situ hybridization data. This study demonstrated that selected reaction monitoring allows to accurately quantify protein expression in formalin-fixed paraffin-embedded tissues and represents therefore a powerful approach for biomarker discovery studies. The untargeted mass spectrometry data is available via ProteomeXchange whereas the quantification data by selected reaction monitoring is available on the Panorama Public website.MS based proteomics has traditionally been used to investigate complex biological systems, such as cell lines, plasma, or fresh-frozen tissues (1, 2). In the last decade however, MS proteomics has extended to the analysis of formalin-fixed paraffin-embedded (FFPE)¹ tissues (3). Formalin fixation is the gold standard for sample storage in clinical pathology because it allows optimal preservation of the morphological features of the tissue and it is economically attractive (storage at room temperature over several years or decades) (4). Several studies have shown that although the individual peptides retrieved and identified from fresh-frozen and FFPE tissues may differ, the biological information obtained from both types of material in terms of number of proteins identified, cellular location and molecular function is very similar (5–10). A number of proteomics studies were reported, which used untargeted MS on FFPE tissues to compare diseased and healthy samples in the search for potential novel biomarkers (10). Nevertheless, these untargeted MS workflows do not allow performing accurate protein quantification on large numbers of samples. One option is to use targeted MS approaches, such as selected reaction monitoring (SRM), which are highly quantitative and reproducible over many samples (11, 12). Additionally, SRM assays allow a high level of multiplexing (several hundreds of peptides can be measured in parallel in a single analysis) (13). The lack of access to a sufficient number of high-quality samples annotated with comprehensive clinical data sets may be a limiting factor for preclinical exploratory phase biomarker studies (14). The possibility to use FFPE samples for MS-based proteomics, in particular for quantitative targeted approaches, would therefore open tremendous perspectives for performing large retrospective biomarker discovery and verification studies. Indeed, in addition to being widely available, most FFPE tissues are annotated with clinical data. Moreover, targeted MS workflows applied to FFPE samples are complementary to techniques requiring high-quality antibodies, such as immunohistochemistry (IHC) or reverse-phase protein arrays (RPPA). These techniques all rely on the measurement of the target protein, with SRM measuring one or ideally several peptides as surrogates of the protein (15, 16). In opposition to IHC and RPPA however, SRM does not rely on the presence of a specific antibody for analyte detection, thereby avoiding cross-reaction issues and making assay development relatively rapid and cost effective. Although SRM is less advanced for protein analysis than for small molecules quantification, the technique was demonstrated to be selective, reproducible, and highly quantitative over large dynamic ranges for proteins as well (17–19). However, although the equivalence of qualitative analyses performed on fresh-frozen and FFPE samples has been investigated and demonstrated, only a few studies evaluated quantitative targeted MS approaches in FFPE samples (20, 21). Targeted proteomics performed on FFPE tissues is still in its early days and known limitations of this technique include the loss of morphologic features of the tissue and an extensive sample preparation, causing a low sample throughput (20). Moreover, targeted proteomics quantifies peptides as surrogates of a protein, with the former not necessarily agreeing in absolute terms with the latter. This is true for bottom-up proteomics in general, but it is of particular importance for FFPE tissues.In this study, we critically assessed the validity of targeted MS applied to peptide quantification in FFPE tissues. We developed and evaluated an SRM assay for the quantification of six peptides of the human receptor tyrosine-protein kinase erbB-2 (HER2) and compared the obtained results with those of standard methods used in clinical pathology, namely IHC and fluorescence in situ hybridization (FISH). HER2 was chosen as a candidate protein because its overexpression is routinely assessed in breast tumors in order to determine susceptibility to anti-HER2 treatment (22). Depending on the laboratory, HER2 overexpression can be assessed by IHC or the amplification of the corresponding gene (ERBB2) can be quantified by FISH (23). Several laboratories use both techniques for decision-making, as they are complementary.In a first step, we developed an SRM assay for the quantification of HER2 peptides in archival clinical FFPE tumor tissues and assessed its analytical performance, including linearity, precision and lower limit of quantification (LLOQ). We then demonstrated the applicability of the method by quantifying HER2 peptides in a cohort of 40 FFPE tumor tissues expressing different levels of HER2 (selected based on ERBB2 gene amplification status). The samples originated from surgical resections performed on women with invasive mammary carcinomas. We thereby investigated several options to normalize the results in regard to sample size. Finally, in order to confirm the validity of SRM as a suitable method for protein quantification in FFPE tissues, we determined the agreement between data generated by SRM and data generated by IHC or FISH.     

同位素稀释法在绝对定量蛋白质组中的研究进展

绝对定量蛋白质组是指基于蛋白质组学方法对细胞、组织或体液中的蛋白质进行绝对量或浓度测定．目前,常用的绝对定量方法主要有基于同位素稀释法的蛋白质组学绝对定量方法和基于质谱数据统计分析的非标记方法．基于同位素稀释法的绝对定量方法是用已知量的同位素标记物对与其混合的样本蛋白质浓度进行测定．常见的同位素标记物包括：由AQUA法、QconCAT法产生的特异性水解肽段,由PSAQ法、Absolute SILAC法产生的标记蛋白和由PrESTs-SILAC法产生的蛋白抗原表位标签．由于同位素稀释法可以对蛋白质进行准确和精确定量,对于临床疾病的诊断和治疗具有明显的现实意义．本文对同位素稀释法在绝对定量蛋白质组中的研究进展及其优缺点和最新应用进行了评述．     

Rapid and Simultaneous Quantification of Levetiracetam and Its Carboxylic Metabolite in Human Plasma by Liquid Chromatography Tandem Mass Spectrometry

A simple liquid chromatography tandem mass spectrometry method was developed and validated according to the guidelines of the US Food and Drug Administration and the European Medicines Agency for a simultaneous quantification of levetiracetam (LEV) and its metabolite, UCB L057 in the plasma of patients. A 0.050 mL plasma sample was prepared by a simple and direct protein precipitation with 0.450 mL acetonitrile (ACN) containing 1 µg/mL of internal standard (IS, diphenhydramine), then vortex mixed and centrifuged. A 0.100 mL of the clear supernatant was diluted with 0.400 mL water and well mixed. A 0.010 mL of the resultant solution was injected into an Agilent Zorbax SB-C18 (2.1 mm×100 mm, 3.5 µm) column with an isocratic elution at 0.5 mL/min using a mixture of 0.1% formic acid in water and ACN (40∶60 v/v). Detection was performed using an AB Sciex API 3000 triple quadrupole mass spectrometer, equipped with a Turbo Ion Spray source, operating in a positive mode: LEV at transition 171.1>154.1, UCB L057 at 172.5>126.1, and IS at 256.3>167.3; with an assay run time of 2 minutes. The lower limit of quantification (LLOQ) for both LEV and UCB L057 was validated at 0.5 µg/mL, while their lower limit of detection (LOD) was 0.25 µg/mL. The calibration curves were linear between 0.5 and 100 µg/mL for both analytes. The inaccuracy and imprecision of both intra-assay and inter-assay were less than 10%. Matrix effects were consistent between sources of plasma and the recoveries of all compounds were between 100% and 110%. Stability was established under various storage and processing conditions. The carryovers from both LEV and UCB L057 were less than 6% of the LLOQ and 0.13% of the IS. This assay method has been successfully applied to a population pharmacokinetic study of LEV in patients with epilepsy.     

Peptide Production and Decay Rates Affect the Quantitative Accuracy of Protein Cleavage Isotope Dilution Mass Spectrometry (PC-IDMS)

No consensus has been reached on the proper time to add stable-isotope labeled (SIL) peptides in protein cleavage isotope dilution mass spectrometry workflows. While quantifying 24 monolignol pathway enzymes in the xylem tissue of Populus trichocarpa, we compared the protein concentrations obtained when adding the SIL standard peptides concurrently with the enzyme or after quenching of the digestion (i.e. postdigestion) and observed discrepancies for nearly all tryptic peptides investigated. In some cases, greater than 30-fold differences were observed. To explain these differences and potentially correct for them, we developed a mathematical model based on pseudo-first-order kinetics to account for the dynamic production and decay (e.g. degradation and precipitation) of the native peptide targets in conjunction with the decay of the SIL peptide standards. A time course study of the digests confirmed the results predicted by the proposed model and revealed that the discrepancy between concurrent and postdigestion introduction of the SIL standards was related to differential decay experienced by the SIL peptide and the native peptide in each method. Given these results, we propose concurrent introduction of the SIL peptide is most appropriate, though not free from bias. Mathematical modeling of this method reveals that overestimation of protein quantities would still result when rapid peptide decay occurs and that this bias would be further exaggerated by slow proteolysis. We derive a simple equation to estimate the bias for each peptide based on the relative rates of production and decay. According to this equation, nearly half of the peptides evaluated here were estimated to have quantitative errors greater than 10% and in a few cases over 100%. We conclude that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification.     

Stable Carbon Isotope Ratios of Lipid Biomarkers of Sulfate-Reducing Bacteria

We examined the potential use of natural-abundance stable carbon isotope ratios of lipids for determining substrate usage by sulfate-reducing bacteria (SRB). Four SRB were grown under autotrophic, mixotrophic, or heterotrophic growth conditions, and the δ¹³C values of their individual fatty acids (FA) were determined. The FA were usually ¹³C depleted in relation to biomass, with Δδ¹³C_{(FA − biomass)} of −4 to −17‰; the greatest depletion occurred during heterotrophic growth. The exception was Desulfotomaculum acetoxidans, for which substrate limitation resulted in biomass and FA becoming isotopically heavier than the acetate substrate. The δ¹³C values of FA in Desulfotomaculum acetoxidans varied with the position of the double bond in the monounsaturated C₁₆ and C₁₈ FA, with FA becoming progressively more ¹³C depleted as the double bond approached the methyl end. Mixotrophic growth of Desulfovibrio desulfuricans resulted in little depletion of the i17:1 biomarker relative to biomass or acetate, whereas growth with lactate resulted in a higher proportion of i17:1 with a greater depletion in ¹³C. The relative abundances of 10Me16:0 in Desulfobacter hydrogenophilus and Desulfobacterium autotrophicum were not affected by growth conditions, yet the Δδ¹³C_{(FA − substrate)} values of 10Me16:0 were considerably greater during autotrophic growth. These experiments indicate that FA δ¹³C values can be useful for interpreting carbon utilization by SRB in natural environments.     

Reverse-Polynomial Dilution Calibration Methodology Extends Lower Limit of Quantification and Reduces Relative Residual Error in Targeted Peptide Measurements in Blood Plasma

Matrix effect is the alteration of an analyte''s concentration-signal response caused by co-existing ion components. With electrospray ionization (ESI), matrix effects are believed to be a function of the relative concentrations, ionization efficiency, and solvation energies of the analytes within the electrospray ionization droplet. For biological matrices such as plasma, the interactions between droplet components is immensely complex and the effect on analyte signal response not well elucidated. This study comprised of three sequential quantitative analyses: we investigated whether there is a generalizable correlation between the range of unique ions in a sample matrix (complexity); the amount of matrix components (concentration); and matrix effect, by comparing an E. coli digest matrix (∼2600 protein proteome) with phospholipid depleted human blood plasma, and unfractionated, nondepleted human plasma matrices (∼10⁷ proteome) for six human plasma peptide multiple reaction monitoring assays. Our data set demonstrated analyte-specific interactions with matrix complexity and concentration properties resulting in significant ion suppression for all peptides (p < 0.01), with nonuniform effects on the ion signals of the analytes and their stable-isotope analogs. These matrix effects were then assessed for translation into relative residual error and precision effects in a low concentration (∼0–250 ng/ml) range across no-matrix, complex matrix, and highly complex matrix, when a standard addition stable isotope dilution calibration method was used. Relative residual error (%) and precision (CV%) by stable isotope dilution were within <20%; however, error in phospholipid-depleted and nondepleted plasma matrices were significantly higher compared with no-matrix (p = 0.006). Finally a novel reverse-polynomial dilution calibration method with and without phospholipid-depletion was compared with stable isotope dilution for relative residual error and precision. Reverse-polynomial dilution techniques extend the Lower Limit of Quantification and reduce error (p = 0.005) in low-concentration plasma peptide assays and is broadly applicable for verification phase Tier 2 multiplexed multiple reaction monitoring assay development within the FDA-National Cancer Institute (NCI) biomarker development pipeline.Plasma is the overriding human medium sampled for established and novel protein biomarkers (1, 2). As of 2011, 1929 high-confidence proteins have been cataloged by the Human Plasma Proteome Project, with estimates that there are up to 10⁷ unique protein sequences in plasma that span a concentration range across 10 orders of magnitude (1, 3). 99% of the protein mass in plasma is made up of 22 proteins including Albumin, Fibrinogen, and a range of immunoglobulins, leaving more than 1900 known small proteins and essentially the entirety of the projected plasma proteome in the remaining 1% (4). It is these low-mass, low abundance proteins such as the Interleukins, C-Reactive Protein, and Carcinoma Antigen 125 (CA125), that are indicative of many important physiological and pathological processes, and proteomic scientists and clinicians have thus focused their efforts in qualitatively and quantitatively defining this fraction for novel biomarkers (4–6).The development of plasma biomarkers is a large-scale undertaking that spans discovery, verification, and validation phases in a multistage pipeline: Thousands of “discovered” differentiated proteins are evaluated for probability of effect, from which 10–100s of proteins are then selected for targeted quantification in verification phase to evaluate sensitivity and specificity for its intended indication (2, 7). Finally a panel of the strongest marker candidates is progressed to validation phase, and FDA-level validated quantitative assays are used to test the clinical utility of the biomarker panel. Liquid Chromatography coupled with Tandem Mass Spectrometry (LC-MS/MS)¹ is the most robust analytical method available for proteomic scientists in this pipeline, able to separate complex mixtures and specifically and sensitively identify and quantify its components (2, 7–10), The ability to ionize and evaporate the contents of a liquid sample (coupling LC to MS/MS) is the basis that allows this to happen (9). Electrospray Ionization (ESI) is the most widely used ionization apparatus in LC-MS/MS bioanalysis because of its ionization efficiency and stability and low chemical specificity (9, 10). Although these properties make ESI very robust, the complexity of biological matrices poses a significant challenge for LC-ESI-MS/MS-based quantitation; despite chromatography and nanospray technology, the ESI droplet of a plasma peptide-digest sample (given its immense range of unique protein/peptide sequences and concentrations) can contain an unknown multitude of co-eluting components that “compete” to dissolve from the droplet and reach gas phase, suppressing and varying the signal intensity responses for a given analyte concentration (9–13). These ionization competing elements can also go on to produce isobaric signals in the third quadrupole that interfere with an analyte''s transition signals (14). Termed “matrix effects,” these phenomena of complex sample matrices can significantly impede quantitative accuracy (15). For high-throughput clinical assays, matrix effects are controlled for by preparing calibration standards in the same biological matrix to mimic the conditions of the samples intended for study as per FDA bioanalytical method validation guidelines (16). The catch to this technique is that the signal from the endogenous analyte in the background matrix hinders accuracy when the nominal concentration is close to or below the endogenous signal (14, 17). There is a need for broadly applicable methods of controlling matrix effects and increasing accuracy in low concentration MRM peptide assays for nondepleted, unfractionated plasma that can be adopted for the highly multiplexed, high throughput, “Tier 2” MS assays required in verification phase of the biomarker development pipeline (2, 8). Several simple methods have independently demonstrated the ability to increase accuracy in various hyphenated-MS assays in complex matrices: “Reverse” curves utilize the stable-isotope analog not as an internal standard but as a surrogate calibration analyte to circumvent interference from the endogenous analyte signal and extend assay Lower Limit(s) of Quantification (LLOQ), and nonlinear calibration techniques have proven to more accurately reflect the concentration-MS detector response at the low and high end of concentration gradients (8, 14, 18–21). Specifically in the case of biological matrices, phospholipids are particularly deleterious ion suppressing elements because of their easily ionizable, polar, and hydrophobic moieties that can have complex interactions with co-eluting analytes as well as the chromatography stationary and mobile phases required for most other analytes (22–25). Combination solid-phase extraction (SPE) and phospholipid removal techniques have proved to effectively minimize ion suppression effects in ESI-MS assays (22–25).In this study, we investigated whether there is a generalizable linear correlation between the number of unique ions (complexity) in a biological sample matrix, the amount of ionizable matrix content (concentration), and matrix effects, for six human plasma peptides comparing serial dilutions of an Escherichia Coli (E. coli) peptide-digest against phospholipid-depleted and nondepleted unfractionated human plasma peptide-digest (highly complex) matrices. We examined the influence of matrix effects on relative residual error in a low-concentration (∼0–250 ng/ml) plasma peptide range, and compared the utility of a reverse-polynomial dilution (RPD) calibration method versus standard addition stable-isotope dilution (SID) in phospholipid-depleted and nondepleted unfractionated human plasma. A peptide-centric matrix effect is reported and the effect of the endogenous analyte signal on relative residual error in low-concentration (∼0–250 ng/ml) plasma peptide assays is established. A RPD calibration technique that extends LLOQ and reduces relative residual error in low-concentration plasma peptide MRM assays is presented.     

双向电泳-质谱技术筛选肝癌血清标记物

采用双向电泳 - 质谱技术筛选肝癌特异的血清蛋白标记物,以利于肝癌的早期诊断和治疗 . 肝癌、肝炎和正常三组各 20 例血清先采用超声、高丰度蛋白去除、脱盐预处理以优化双向电泳,图像分析三组血清图谱寻找差异点,基质辅助激光解吸飞行时间质谱对差异点进行鉴定 . 结果显示,通过样品预处理,血清上样体积平均增加 3 ～ 4 倍,参考胶点数由 218 个增至 332 个,白蛋白和免疫球蛋白明显减弱,水平条带明显减少 . 图谱比较所得 37 个差异点,经鉴定为 7 种蛋白 . 与正常组比较,转铁蛋白、甲状腺素运载蛋白在肝炎和肝癌组低表达,α-1 抗胰蛋白酶、凝聚素、铜蓝蛋白、触珠蛋白在肝炎和肝癌组均高表达 . α-1 抗胰蛋白酶在肝癌组较肝炎组高表达,而热休克蛋白 27 只在肝癌组表达 . 上述结果提示,双向电泳-质谱技术可发现肝癌发生发展过程中血清蛋白表达谱质或量的变化,从而为肝癌的早期诊断及治疗奠定基础 .     

Tracing Cationic Nutrients from Xylem into Stem Tissue of French Bean by Stable Isotope Tracers and Cryo-Secondary Ion Mass Spectrometry

Fluxes of mineral nutrients in the xylem are strongly influenced by interactions with the surrounding stem tissues and are probably regulated by them. Toward a mechanistic understanding of these interactions, we applied stable isotope tracers of magnesium, potassium, and calcium continuously to the transpiration stream of cut bean (Phaseolus vulgaris) shoots to study their radial exchange at the cell and tissue level with stem tissues between pith and phloem. For isotope localization, we combined sample preparation with secondary ion mass spectrometry in a completely cryogenic workflow. After 20 min of application, tracers were readily detectable to various degrees in all tissues. The xylem parenchyma near the vessels exchanged freely with the vessels, its nutrient elements reaching a steady state of strong exchange with elements in the vessels within 20 min, mainly via apoplastic pathways. A slow exchange between vessels and cambium and phloem suggested that they are separated from the xylem, parenchyma, and pith, possibly by an apoplastic barrier to diffusion for nutrients (as for carbohydrates). There was little difference in these distributions when tracers were applied directly to intact xylem via a microcapillary, suggesting that xylem tension had little effect on radial exchange of these nutrients and that their movement was mainly diffusive.Long-distance transport of nutrients in stems is strongly influenced by the interaction of the moving xylem sap with the surrounding tissues (e.g. phloem; Stout and Hoagland, 1939; Biddulph and Markle, 1944). The importance of this radial exchange was highlighted in studies on budgets of carbon/nitrogen and mineral nutrients (Pate et al., 1979; Jeschke et al., 1985, 1991; Wolf et al., 1991). The composition of a solution is changed during perfusion of stem pieces (Gilmer and Schurr, 2007), suggesting that xylem sap composition is regulated. Thus, the fluxes of nutrients in the xylem could be regulated through the ionic concentration and also from the influence of nutrient concentration (e.g. potassium) on hydraulic properties (Thompson and Zwieniecki, 2005). The transport of these nutrients in stems, therefore, does not occur in a simple pipeline connecting roots with leaves but in pathways that involve many tissues in the stem, in the same way that photoassimilate transport is not confined to sieve tubes (van Bel, 2003). However, perfusion experiments with stem pieces may be inappropriate for elucidating these interactions (van Ieperen, 2007), since lateral flow may be promoted by the unnatural pressure regime. This reservation also applies when the root pressure chamber is used to extract sap, for example, in experiments that showed strong interactions between xylem and adjacent tissues (Siebrecht et al., 2003; Gilmer and Schurr, 2007). Therefore, studies of nutrient and water movement in the xylem should use techniques that minimize any perturbation of the water status of all stem tissues.Isotope tracers are ideal for studies toward a mechanistic understanding of nutrient exchange between the transpiration stream and different stem tissues, because they are chemically identical to the traced elements. Enriched stable isotopes are available for most nutrients and can be detected at subcellular spatial resolution with imaging mass spectrometric techniques such as secondary ion mass spectrometry (SIMS), provided that the distribution of diffusible tracers can be preserved until completion of the analysis. Strict cryogenic sample preparation followed by analysis with SIMS below −130°C (cryo-SIMS) has been shown to satisfy this criterion (Metzner et al., 2008), with scanning electron microscopy of the frozen samples (cryo-SEM) for quality control and detailed anatomical information of the individual tissues.Here, we used this cryogenic protocol to examine the exchange between xylem vessels and stem tissue of French bean (Phaseolus vulgaris ‘Fardenlosa Shiny’), with stable isotope tracers for potassium, calcium, and magnesium applied to the transpiration stream of a cut shoot. Based on earlier microanalytical studies on the diffusion kinetics of cationic nutrients moving into roots (Kuhn et al., 2000; Horst et al., 2007), we selected two different periods of tracer application, namely 20 min to show any potential diffusion barriers and 240 min to show distribution patterns after reaching a steady state in nutrient exchange between xylem and surrounding tissue. We evaluated our standard method of tracer application, via the cut stem, in which stem water status was disturbed, in an ancillary experiment where the solution entered via microcapillary directly into xylem under tension.