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Although reproductive factors have been repeatedly associated with lung cancer risk, no study to date has directly evaluated the relationship with endogenous sex hormones nor with aromatase activity in postmenopausal never-smoking women. A case-control study of 397 incident lung cancer cases and their individually matched controls, nested within the Shanghai Women's Health Study, was conducted among postmenopausal women who were lifetime never smokers. Prediagnostic concentrations of sex hormones was quantitated using LC-MS/MS assays in plasma. The product-substrate molar ratio of estrone to androstenedione was used as an index of aromatase activity (IAA). Multivariable conditional logistic regression models were used to calculate odds ratios (ORs) for lung cancer. Baseline concentrations of estradiol, free testosterone and IAA were inversely associated with subsequent risk of lung cancer in multivariable-adjusted models. When further adjusted for body mass index, the inverse association with estradiol was attenuated and no longer statistically significant, but the association with free testosterone and IAA remained. In analyses confined to participants having never used menopausal hormone therapy in 376 case-control pairs, the inverse association with free testosterone and IAA was slightly strengthened. OR for the highest vs the lowest quartile of free testosterone was 0.55 (95% CI = 0.34-0.90; P

N-terminal sequence of parathyroid hormone-related protein (PTHrP) has close homology to parathyroid hormone (PTH). In health, both PTH and PTHrP participate in calcium regulation and homeostasis, but some of the functions, such as regulation of bone development, teeth eruption, calcium regulation in central nervous system, and calcium regulation during pregnancy and fetal development, are unique to PTHrP. In pathology, PTHrP is involved in activation of the pathways, allowing tumor cells to form bone metastasis. In contemporary clinical practice, measurements of PTHrP are used for diagnosing and management of patients suspected of hypercalcemia of malignancy. We describe high-sensitivity, high-specificity LC-MS/MS method for measurement of PTHrP. Sample preparation in this method is performed as follows: internal standard (

Measurement of methylmalonic acid (MMA) plays an important role in the diagnosis of vitamin B

BACKGROUND Hemoglobinopathies and thalassemias are the most common genetically determined disorders. Current screening methods include cation-exchange HPLC and electrophoresis, the results of which can be ambiguous because of limited resolving power. Subsequently, laborious genetic testing is required for confirmation. METHODS We performed a top-down tandem mass spectrometry (MS/MS) approach with a fast data acquisition (3 min), ultrahigh mass accuracy, and extensive residue cleavage by use of positive electrospray ionization 21 Tesla Fourier transform ion cyclotron resonance–tandem mass spectrometry (21 T FT-ICR MS/MS) for hemoglobin (Hb) variant de novo sequencing and β-thalassemia diagnosis. RESULTS We correctly identified all Hb variants in blind analysis of 18 samples, including the first characterization of homozygous Hb Himeji variant. In addition, an Hb heterozygous variant with isotopologue mass spacing as small as 0.0194 Da (Hb AD) was resolved in both precursor ion mass spectrum (MS1) and product ion mass spectrum (MS2). In blind analysis, we also observed that the abundance ratio between intact δ and β subunits (δ/β) or the abundance ratio between intact δ and α subunits (δ/α) could serve to diagnose β-thalassemia trait caused by a mutation in 1 HBB gene. CONCLUSIONS We found that 21 T FT-ICR MS/MS provides a benchmark for top-down MS/MS analysis of blood Hb. The present method has the potential to be translated to lower resolving power mass spectrometers (lower field FT-ICR mass spectrometry and Orbitrap) for Hb variant analysis (by MS1 and MS2) and β-thalassemia diagnosis (MS1).

Harmonization of diagnostic test results is fundamental to the effective use of laboratory testing in the diagnosis, treatment, and monitoring of disease. Formal approaches to harmonization and standardization provide a rigorous and high-quality roadmap to this end, although the formal harmonization process can be long and complex. In the meantime, more informal approaches to harmonization can provide a useful pathway to improved harmonization in the short term. Factors relevant to harmonization are discussed with particular attention to protein assays using LC-MS/MS. Published formal and informal harmonization projects are provided as examples, including lessons drawn from these projects.

Motivation Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don’t access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement. This method utilizes both isotope distribution and changes in neutromer spacing, which benefits the analysis of both concentration and turnover. Results We have developed a data analysis tool, DeuteRater, to measure protein turnover from metabolic D2O labeling. DeuteRater uses theoretical predictions for label-dependent change in isotope abundance and inter-peak (neutromer) spacing within the isotope envelope to calculate protein turnover rate. We have also used these metrics to evaluate the accuracy and precision of peptide measurements and thereby determined the optimal data acquisition parameters of different instruments, as well as the effect of data processing steps. We show that these combined measurements can be used to remove noise and increase confidence in the protein turnover measurement for each protein. Availability and Implementation Source code and ReadMe for Python 2 and 3 versions of DeuteRater are available at https://github.com/JC-Price/DeuteRater. Data is at https://chorusproject.org/pages/index.html project number 1147. Critical Intermediate calculation files provided as Tables S3 and S4. Software has only been tested on Windows machines. Supplementary information Supplementary data are available at Bioinformatics online.

HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM-resistant, DM-dependent, or DM-sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ-peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T-cell epitopes to DM editing.

Steroid concentrations in stimulated follicular fluid (sFF) samples have been linked to the quality of oocytes used in IVF treatments. Most of the published studies focused on evaluating the association of the IVF outcomes with only a few of the steroids, measured by immunoassays (IA). We performed a treatment outcome, prospective cohort study using stimulated FF sampled from 14 infertile women undergoing IVF treatment; single oocyte was used per IVF cycle. Fourteen endogenous steroids were analyzed in 22 ovarian follicle aspirations, which corresponded to the embryos used in the IVF. Ten oocytes were associated with live birth (LB) and 12 with no pregnancy (NP). Steroids were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. Differences in distribution of concentrations in association with the pregnancy outcome (LB or NP), and receiver operating characteristic (ROC) curves analysis were performed for the entire cohort and for within-women data. The predominant androgen and estrogen in stimulated sFF were androstenedione (A4) and estradiol (E2), respectively. Lower concentrations of pregnenolone (Pr), lower ratios of A4/ dehydroepiandrosterone (DHEA), testosterone (Te)/DHEA, and greater ratios of E2/Te, and estrone/A4 were observed in sFF samples associated with LB. Among the oocytes associated with NP, in four out of 12 samples total concentration of androgens was above the distribution of the concentrations in the oocytes corresponding to the LB group. Observations of the study indicated increased consumption of precursors and increased biosynthesis of estrogens in the follicles associated with LB. Our data suggest that potentially steroid profiles in sFF obtained during oocyte retrieval may serve as biomarkers for selection of the best embryo to transfer after IVF.

To improve efficiency in our mass spectrometry laboratories we have made efforts to reduce the number of calibration standards utilized for quantitation over time. We often analyze three or more batches of 96 samples per day, on a single instrument, for a number of assays. With a conventional calibration scheme at six concentration levels this amounts to more than 5000 calibration points per year. Modern LC-tandem mass spectrometric instrumentation is extremely rugged however, and isotopically labelled internal standards are widely available. This made us consider whether alternative calibration strategies could be utilized to reduce the number of calibration standards analyzed while still retaining high precision and accurate quantitation. Here we demonstrate how, by utilizing a single calibration point in each sample batch, and using the resulting response factor (RF) to update an existing, historical response factor (HRF), we are able to obtain improved precision over a conventional multipoint calibration approach, as judged by quality control samples. The laboratory component of this study was conducted with an existing LC tandem mass spectrometric method for three androgen analytes in our production laboratory. Using examples from both simulated and laboratory data we illustrate several aspects of our single point alternative calibration strategy and compare it with a conventional, multipoint calibration approach. We conclude that both the cost and burden of preparing multiple calibration standards with every batch of samples can be reduced while at the same time maintaining, or even improving, analytical quality.

HLA-DM is essential for editing peptides bound to MHC class II, thus influencing the repertoire of peptides mediating selection and activation of CD4(+) T cells. Individuals expressing HLA-DQ2 or DQ8, and DQ2/8 trans-dimers, have elevated risk for type 1 diabetes (T1D). Cells coexpressing DM with these DQ molecules were observed to express elevated levels of CLIP (Class II associated invariant chain peptide). Relative resistance to DM-mediated editing of CLIP was further confirmed by HPLC-MS/MS analysis of eluted peptides, which also demonstrated peptides from known T1D-associated autoantigens, including a shared epitope from ZnT8 that is presented by all four major T1D-susceptible DQ molecules. Assays with purified recombinant soluble proteins confirmed that DQ2-CLIP complexes are highly resistant to DM editing, whereas DQ8-CLIP is partially sensitive to DM, but with an apparent reduction in catalytic potency. DM sensitivity was enhanced in mutant DQ8 molecules with disruption of hydrogen bonds that stabilize DQ8 near the DM-binding region. Our findings show that T1D-susceptible DQ2 and DQ8 share significant resistance to DM editing, compared with control DQ molecules. The relative resistance of the T1D-susceptible DQ molecules to DM editing and preferential presentation of T1D-associated autoantigenic peptides may contribute to the pathogenesis of T1D.

There are at least two valid approaches to the thermodynamics of electrons in metals. One takes a microscopic view, based on models of electrons in metals and superconductor and uses statistical mechanics to calculate the total thermodynamic functions for the model-based system. Another uses partial molar quantities, which is a rigorous thermodynamic method to analyze systems with components that can cross phase boundaries and is particularly useful when applied to a system composed of interacting components. Partial molar quantities have not been widely used in the field of solid state physics. The present paper will explore the application of partial molar electronic entropy and partial molar electronic heat capacity to electrons in metals and superconductors. This provides information that is complementary information from other approaches to the thermodynamics of electrons in metals and superconductors and can provide additional insight into the properties of those materials. Furthermore, the application of partial molar quantities to electrons in metals and superconductors has direct relevance to long-standing problems in other fields, such as the thermodynamics of ions in solution and the thermodynamics of biological energy transformations. A unifying principle between reversible and irreversible thermodynamics is also discussed, including how this relates to the completeness of thermodynamic theory.

We thank Dr. Laszlo Prokai, Dr. Jae-Seok Kim, and Dr. Hyun Sik Kim for their insightful editorial commentaries on our recent publication “ Diagnosis of hemoglobinopathy and β-thalassemia by 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry of hemoglobin from blood ” (1-3). As described by the editorial authors, 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry (21 T FT-ICR MS) and top-down MS/MS set a new benchmark for precision diagnosis of hemoglobinopathies and thalassemia with fast sample preparation (dilute and infuse) and data acquisition (3 min).

Leflunomide is a prodrug that is metabolized to the active metabolite, teriflunomide (A77 1726), to inhibit the enzyme dihydroorotate dehydrogenase and decrease the synthesis of pyrimidine nucleotides for DNA and RNA synthesis. Teriflunomide is primarily used for the treatment of rheumatoid arthritis and multiple sclerosis.A liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed and validated to quantify the drug teriflunomide over a concentration range of 5 ng/mL-200 μg/mL in serum or plasma. The calibration curve was divided into two separate overlapping regions of the analytical measurement range, with a high curve and a low curve range. Samples are first analyzed using the high-range calibration curve after a 100-fold dilution of the sample extract. Samples falling below the upper curve region are evaluated again without dilution and quantified, if possible, against the low curve calibration standards. This method can be used to support therapeutic drug monitoring of patients that are administered with leflunomide therapy.

Leflunomide is a prodrug that is metabolized to the active metabolite, teriflunomide (A77 1726), to inhibit the enzyme dihydroorotate dehydrogenase and decrease the synthesis of pyrimidine nucleotides for DNA and RNA synthesis. Teriflunomide is primarily used for the treatment of rheumatoid arthritis and multiple sclerosis.A liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed and validated to quantify the drug teriflunomide over a concentration range of 5 ng/mL-200 μg/mL in serum or plasma. The calibration curve was divided into two separate overlapping regions of the analytical measurement range, with a high curve and a low curve range. Samples are first analyzed using the high-range calibration curve after a 100-fold dilution of the sample extract. Samples falling below the upper curve region are evaluated again without dilution and quantified, if possible, against the low curve calibration standards. This method can be used to support therapeutic drug monitoring of patients that are administered with leflunomide therapy.

BACKGROUND: Parathyroid hormone-related protein (PTHrP) is involved in intracellular calcium regulation, neural cell proliferation and synaptic transmission. To date, no studies have been performed to evaluate the potential of PTHrP concentrations in cerebrospinal fluid (CSF) as a biomarker of brain pathophysiology. In this study we evaluated the association between CSF concentrations of PTHrP with the core CSF biomarkers of Alzheimer’s disease (AD). METHODS: PTHrP and calcium were analysed using validated mass spectrometry based methods in a set of CSF samples that tested positive (n = 45) and negative (n = 45) for the AD biomarkers, including total tau protein (T-tau), phosphorylated tau protein (P-tau) and amyloid-β 42 (Aβ42). The measured CSF concentrations of PTHrP and calcium (Ca) were evaluated for association with AD CSF biomarkers. RESULTS: PTHrP and Ca concentrations in CSF samples ranged between 25 and 137 pmol/L and 0.92–1.53 mmol/L, respectively. Higher concentrations of PTHrP were observed in association with increased concentrations of T-tau and P-tau in the AD and the control group; while a stronger correlation was observed in the control group (ρ = 0.6, p

Background A liquid chromatography tandem mass spectrometry (LC-MS/MS) method has been validated for use in therapeutic monitoring of the drug leflunomide in human serum and plasma. Because of concerns of teratogenicity, it is recommended that women who want to become pregnant have concentrations below 0.02 mcg/mL, although therapeutic levels are generally greater than 20 mcg/mL. Consequently, the method required a 40,000-fold dynamic range, which was achieved by dividing the curve range into 2 separate regions but with a single extraction procedure used for both. Methods A chromatographic separation was achieved between the parent drug and the active metabolite, teriflunomide (A77 1726), and the latter was quantified across a quantitative range of 0.005-200 mcg/mL. Samples were evaluated in an upper curve region first, with dilution, to determine whether the drug concentrations were in an appropriate therapeutic range. Samples that fell below the upper region were then reevaluated in the lower region without dilution. Results The method was shown to be reliable, with good accuracy and precision statistics, and acceptable quantitation using 4 different collection tube types. Mean accuracy over 6 control concentrations was within 5.4%, over 5 validation runs, whereas %coefficient of variation (CV) was within 8.15%. Evaluation of sodium heparin, KEDTA, NaF/K oxalate, and plain serum tubes from 6 separate individuals at the lower limit of quantification (LLOQ) showed no influence on the ability to quantify teriflunomide accurately. Regression equations for a curve range of 0.005-1 mcg/mL gave R values of 0.998 or better, whereas the range 0.8-200 mcg/mL had R values of 0.997 or better. Conclusions The authors have developed and validated a method that allows quantification of leflunomide across a 40,000-fold range of 0.005-200 mcg/mL.

Challenges for steroid analysis by LC-MS/MS include low ionization efficiency, endogenous isobars with similar fragmentation patterns and chromatographic retention. Differential ion mobility spectrometry (DMS) provides an additional degree of separation prior to MS/MS detection, and shows promise in improving specificity of analysis. We developed a sensitive and specific method for measurement of corticosterone, 11-deoxycortisol, 11-deoxycorticosterone, 17-hydroxyprogesterone and progesterone in human serum and plasma using an ABSciex 5500 mass spectrometer equipped with a differential ion mobility interface.250μL aliquots of serum were spiked with deuterated internal standards and extracted with MTBE. The samples were analyzed using positive mode electrospray LC-DMS-MS/MS. The method was validated and compared with immunoassays and LC-MS/MS methods of reference laboratories.Inter and intra assay imprecision was10%. Limits of quantification and detection in nmol/L were 0.18, 0.09 for corticosterone and 17-hydroxyprogesterone, 0.30, 0.16 for 11-deoxycortisol, 0.12, 0.06 for progesterone and 0.06, 0.03 for 11-deoxycorticosterone. Comparison for progesterone and 17-hydroxyprogesterone with immunoassay showed slopes of 0.97 and 1.0, intercepts of 0.16 and 0.10 and coefficients of determination (r(2)) of 0.92 and 0.97, respectively. Progesterone by immunoassay showed positive bias in samples measuring3.18nmol/L. Reference intervals for progesterone and 11-deoxycorticosterone in post-menopausal women were found to be2.88 and0.28nmol/L respectively.We developed and validated an LC-DMS-MS/MS method for analysis of five endogenous steroids suitable for routine measurements in clinical diagnostic laboratories. Specificity gained with DMS allows reducing the complexity of sample preparation, decreasing LC run times and increasing speed of the analysis.

A universal relationship between the partial molar entropy of electrons in a conductor and the absolute thermoelectric power of the conductor was previously established using macroscopic thermodynamics. This relationship may depend on temperature but not on the type of material. Building on this, a recent comment published in this journal, as well as some earlier work, has argued that the partial molar entropy of electrons in a conductor is essentially equivalent to the absolute thermoelectric power of the metal. The argument was based on the thermodynamic and transport properties of a free electron Fermi gas. To further validate the relationship the present paper extends this approach to a jellium model of electronic structure. If the proposed equivalence between partial molar entropy and absolute thermoelectric power is valid it opens the way for an experimental thermodynamic method to measure quantities that have previously been considered un-measurable, such as partial molar entropies of ions in solution and electric fields in homogeneous conductors placed in a temperature gradient. It also relates to questions about the completeness of current thermodynamic theory and the possibility of a new principle or law of thermodynamics.

Kjelstrup et al. recently applied non-equilibrium thermodynamics to analyze the thermodynamic relationships for thermo-electrochemical effects in certain electrochemical cells [Electrochim. Acta 99 (2013) 166–175]. The present paper considers whether one can extend such relationships to establish equivalence between certain non-equilibrium thermodynamic properties, such as transported entropies, and equilibrium thermodynamic properties, such as partial molar entropies. If so it would enable the use of thermo-electrochemical measurements to determine certain quantities that have heretofore been considered “un-measurable”, such as partial molar entropies of ions in solution. It would also provide a unifying principle between non-equilibrium thermodynamics and reversible thermodynamics, and it could lead one to consider the possibility of an additional law or principle of thermodynamics.

Effective CD8+ T cell responses depend on presentation of a stable peptide repertoire by MHC class I (MHC I) molecules on the cell surface. The overall quality of peptide–MHC I complexes (pMHC I) is determined by poorly understood mechanisms that generate and load peptides with appropriate consensus motifs onto MHC I. In this article, we show that both tapasin (Tpn), a key component of the peptide loading complex, and the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP) are quintessential editors of distinct structural features of the peptide repertoire. We carried out reciprocal immunization of wild-type mice with cells from Tpn- or ERAAP-deficient mice. Specificity analysis of T cell responses showed that absence of Tpn or ERAAP independently altered the peptide repertoire by causing loss as well as gain of new pMHC I. Changes in amino acid sequences of MHC-bound peptides revealed that ERAAP and Tpn, respectively, defined the characteristic amino and carboxy termini of canonical MHC I peptides. Thus, the optimal pMHC I repertoire is produced by two distinct peptide editing steps in the endoplasmic reticulum.

The use of negative axial thermal gradients in gas chromatography (TGGC) has intrigued chromatographers since the early 1950s because of the dramatic narrowing of analyte bands and concomitant raised expectations for improving resolving power. However, technical difficulties experienced in construction of TGGC instrumentation and control of the temperature along the column have made its implementation and, hence, detailed study difficult. In this work, we describe a TGGC system capable of rapidly producing and varying thermal gradient profiles by simultaneous use of resistive heating and convective cooling. Heating and cooling rates as high as 1200 and 2500 °C/min, respectively, allowed the creation of dynamic temperature gradients. The separation characteristics of TGGC with dynamically changing temperature gradients are demonstrated. A gradient velocity of 2.22 cm/s provided repetitive separations every 45 s, and injection band widths of 45 s duration were transformed into approximately 1-s peak widths. Peak tailing for basic compounds was nearly eliminated. Dynamic TGGC allows unique control over separations, oftentimes improving resolution and detection signal-to-noise. Thermally controlled elution in TGGC holds great promise for performing smart separations in which the separation time window is most efficiently utilized, and optimized separations can be quickly achieved. Rapid adjustment of relative compound elution can be used to greatly reduce GC method development time.

BACKGROUND Measurement of serum thyroglobulin (Tg) is used to monitor patients after treatment for differentiated thyroid carcinoma (TC). Difficulty in using Tg as a biomarker of the recurrence of TC in many patients stems from the presence of endogenous anti-Tg autoantibodies (Tg-AAbs), which can interfere with immunoassays (IAs) and cause false-negative results. METHODS We enriched Tg from serum samples using rabbit polyclonal anti-Tg antiserum and protein precipitation. Unrelated proteins were partially depleted in the process. Enriched proteins were then denatured, reduced, and digested with trypsin after the addition of a winged internal standard peptide. A Tg-specific tryptic peptide was purified by immunoaffinity extraction and analyzed by 2-dimensional LC-MS/MS. Instrument cycle time was 6.5 min per sample. RESULTS The lower limit of quantification was 0.5 ng/mL (0.76 fmol/mL dimer). Total imprecision of triplicate measurements in serum samples over 5 days was CONCLUSIONS The introduced method has acceptable performance characteristics for use in clinical diagnostic applications. The most substantial disagreement between methods was observed in Tg-AAb–positive samples with concentrations

Numerous molecular effects have been attributed to histone deacetylase inhibitors (HDACI's), including the induction of major histocompatibility (MHC) genes. Here we report that one FDA approved HDACI, Vorinostat, and a second HDACI currently in clinical trials, Entinostat, reduce the ratio of class II associated invariant peptide (CLIP) to the MHC class II molecule, HLA-DR, indicating an increase in the non-CLIP peptides bound to HLA-DR. The HDACI effects are apparent with immortalized B-cells, HLA-DR constitutive melanoma cells and with melanoma cells expressing HLA-DR due to transformation with an expression vector for the HLA-DR gene co-activator, CIITA. Entinostat treatment leads to upregulation of Cathepsin L1, and the HLA-DR peptidome of the Entinostat treated cells is consistent with increased Cathepsin L1 mediated proteolysis. These results indicate that HDACI treatments may alter the HLA-DR peptidome of cells in patients and provide a way to identify novel immunogens for vaccinations and the study of autoantigens.

Leflunomide is a prodrug used primarily for treatment of rheumatoid arthritis. The active metabolite, teriflunomide (A77 1726), inhibits the enzyme dihydroorotate dehydrogenase and thereby reduces the synthesis of pyrimidine ribonucleotides. Teriflunomide is also administered directly and finds use in treating multiple sclerosis. Therapeutic concentrations are generally in the tens of μg/mL serum or plasma and, due to adverse effects and the time required to reach steady state, therapeutic drug monitoring is beneficial. The drug is also a potential teratogen. A method was developed and validated to quantify the drug teriflunomide over a 40,000-fold concentration range of 5 ng/mL to 200 μg/mL in serum or plasma. This is accomplished by dividing the quantitative range into two separate but overlapping regions; a high curve and a low curve range. Samples are evaluated first against the high curve after a 100-fold dilution of the sample extract. Samples falling below the upper curve region are evaluated again without dilution and quantified, if possible, against the low curve calibration standards. Appropriate choice of a concentration for the deuterated internal standard (D4-teriflunomide) allows for a single, identical, extraction procedure to be performed for both curve regions but with the dilution performed for high curve samples. The method is rugged and reliable with good accuracy and precision statistics.

Introduction Burn injury inevitably leads to changes in the endogenous production of cytokines, as well as adrenal and gonadal steroids. Previous studies have reported gender-related differences in outcome following burn injury, which suggests that gonadal steroids may play a role. The aim of this study was to assess alterations in concentration of endogenous steroids in patients with burn injury. Methods For this single-center, prospective descriptive study, high-sensitivity liquid chromatography tandem mass spectrometry (LC-MS/MS)-based steroid quantification was used to determine longitudinal profiles of the concentrations of endogenous steroids in plasma from sixteen adult male patients with burn injury (14.5–72% of total body surface area). Steroids were extracted from plasma samples and analyzed using multiple reaction monitoring acquisition, with electrospray ionization on a triple quadruple mass spectrometer. Total protein concentration was measured in the samples using spectrophotometry. Results Steroid and total protein concentration distributions were compared to reference intervals characteristic of healthy adult men. Concentrations of the following steroids in plasma of burn injured patients were found to correlate positively to the area of the burn injury: cortisol (r = 0.84), corticosterone (r = 0.73), 11-deoxycortisol (r = 0.72), androstenedione (r = 0.72), 17OH-progesterone (r = 0.68), 17OH-pregnenolone (r = 0.64) and pregnenolone (r = 0.77). Concentrations of testosterone decreased during the acute phase and were up to ten-times lower than reference values for healthy adult men, while concentrations of estrone were elevated. By day 21 after injury, testosterone concentrations were increased in younger, but not older, patients. The highest concentrations of estrone were observed on day 3 after the injury and then declined by day 21 to concentrations comparable to those observed on the day of the injury. Conclusion Burn injury alters endogenous steroid biosynthesis, with decreased testosterone concentrations and elevated estrone concentrations, during the first 21 days after the injury. Concentrations of glucocorticoids, progestagens and androgen precursors correlated positively with the area of burn injury. The finding of increased estrone following burn injury needs to be confirmed in a larger hypothesis-driven study.

Measurement of methylmalonic acid (MMA) plays an important role in the diagnosis of vitamin B12 deficiency. Vitamin B12 is an essential cofactor for the enzymatic carbon rearrangement of methylmalonyl-CoA (MMA-CoA) to succinyl-CoA (SA-CoA), and the lack of vitamin B12 leads to elevated concentrations of MMA. Presence of succinic acid (SA) complicates the analysis because mass spectra of MMA and SA are indistinguishable, when analyzed in negative ion mode and the peaks are difficult to resolve chromatographically. We developed a method for the selective analysis of MMA that exploits the significant difference in fragmentation patterns of di-butyl derivatives of the isomers MMA and SA in a tandem mass spectrometer when analyzed in positive ion mode. Tandem mass spectra of di-butyl derivatives of MMA and SA are very distinct; this allows selective analysis of MMA in the presence of SA. The instrumental analysis is performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in positive ion mode, which is, in combination with selective extraction of acidic compounds, is highly selective for organic acids with multiple carboxyl groups (dicarboxylic, tricarboxylic, etc.). In this method organic acids with a single carboxyl group are virtually undetectable in the mass spectrometer; the only organic acid, other than MMA, that is detected by this method is its isomer, SA. Quantitative measurement of MMA in this method is performed using a deconvolution algorithm, which mathematically resolves the signal corresponding to MMA and does not require chromatographic resolution of the MMA and SA peaks. Because of its high selectivity, the method utilizes isocratic chromatographic separation; reconditioning and re-equilibration of the chromatographic column between injections is unnecessary. The above features of the method allow high-throughput analysis of MMA with analysis cycle time of 1 min.

Aliquots of serum or plasma samples are combined with stable isotope labeled internal standard. Pancreatic polypeptide (PP) and its truncated variant PP3-36 are enriched by incubation with anti-PP antibody conjugated to magnetic beads. Peptides are eluted from beads in acidic buffer and the samples analyzed using liquid chromatography coupled with tandem mass spectrometry. Instrumental analysis of PP and PP3-36 is performed using electrospray ionization ESI in positive ion mode and multiple reaction monitoring (MRM) acquisition.

ObjectiveLittle is known about the aetiology of polycystic ovary syndrome (PCOS). Some suggest that elevated maternal androgens during gestation play a causative role. This implies placental passage of androgens during pregnancy. The aim of this study is to compare androgen and estrogen concentrations in maternal serum during pregnancy and in umbilical cord blood, between mothers with PCOS and their offspring compared to controls.DesignProspective case–control study.MethodsMaternal blood samples were collected around 20 weeks of gestation and at delivery. Umbilical cord blood was also taken at delivery. Androgens (testosterone (T), androstenedione (ADION), dehydroepiandrostenedione (DHEA)) and estrogens (estrone (E1), estradiol (E2), estriol (E3)) were measured using the liquid chromatography tandem mass spectrometry (LC-MS/MS) methods.ResultsAt 20 weeks of gestation: T (P=0.019) and ADION (P=0.034) were higher in the PCOS mothers (pregnant with a girl), whereas DHEA, E1, E2, and E3were not different. Maternal concentration at birth: T (P=0.004) and ADION (P=0.009) were also higher in the subgroup of PCOS mothers that were pregnant with a girl compared to the girl pregnancy controls. DHEA, E1, E2and E3were not different. In umbilical cord blood, no differences were found for T, ADION, DHEA, E2, E3, and AMH between the PCOS mothers and the controls respectively. E1was lower in girls from PCOS mothers (P=0.007).ConclusionsDespite elevated maternal androgen concentrations during pregnancy in PCOS mothers, offspring showed no signs of elevated androgen concentrations in cord blood at birth using the latest highly specific LC-MS/MS methods.

We describe a direct method of measurement of free estradiol using equilibrium dialysis followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Serum aliquots and internal standards are extracted by liquid-liquid extraction using methyl-tert-butyl ether (MTBE) followed by derivatization with dansyl chloride. An API 5500 mass spectrometer operated in positive electrospray mode is used for detection.

Controlled ovarian hyperstimulation is performed to assist with generation of multiple mature oocytes for use in in vitro fertilization (IVF). The goal of our study was to evaluate differences in protein and steroid profiles in ovarian follicular fluid (hFF) samples obtained during oocyte retrieval from women undergoing IVF treatment and to identify physiological pathways associated with the proteins. The hFF samples were depleted of abundant proteins, fractionated by ultrafiltration, digested, and analyzed by nano-LC-QTOF. Concentrations of 15 endogenous steroids were determined in the samples using LC-MS/MS methods. The total number of proteins identified in the samples was 75, of which 4, 7, and 2 were unique to the samples from women with viable pregnancy, miscarriage, and no pregnancy, respectively. Identified proteins were associated with the acute response signaling, coagulation system, intrinsic and extrinsic prothrombin activation, complement system, neuroprotective role of THOP1, FXR/RXR activation, role of tissue factor, and growth hormone pathways. A greater number of proteins associated with biosynthesis was found in hFF samples corresponding to the oocytes resulting in pregnancy. The abundance of seven proteins was found to be associated with steroidogenesis. The obtained data will contribute to better understanding of the pathogenesis and development of noninvasive markers for assessment of oocytes viability.

Measurement of free estradiol offers a better representation of the bioactive fraction of the hormone. We describe a direct equilibrium dialysis-liquid chromatography-tandem mass spectrometry (ED-LC-MS/MS) method for serum free estradiol.Two hundred fifty microliter aliquots of serum were dialyzed for 22h followed by liquid-liquid extraction and derivatization with dansyl chloride. Free estradiol was measured using LC-MS/MS with an AB SCIEX 5500 mass spectrometer in positive ion and multiple reaction monitoring (MRM) mode.The limits of detection and quantification for free estradiol were 0.25 and 0.5pg/ml (0.9 and 1.8pmol/l) respectively. Total imprecision was less than 10%. Results of method comparison showed 3 times overestimation using indirect methods of measurement. Reference intervals in pre-menopausal women in follicular, mid-cycle, and luteal phases of cycle were2.4,3.1 and2.6pg/ml (8.8, 11.4, 9.5pmol/l) respectively; in post menopausal women the concentrations were ≤0.5pg/ml (1.8pmol/l).ED-LC-MS/MS is a direct method for accurately measuring free estradiol, independent of total estradiol or sex hormone binding globulin concentrations. Imprecision and sensitivity of the method are adequate for clinical diagnostic applications. The degree of variation observed in the method comparison reinforces the relevance of method specific reference ranges.

Histoplasmosis is a severe dimorphic fungus infection, which is often difficult to diagnose due to similarity in symptoms to other diseases and lack of specific diagnostic tests. Urine samples from histoplasma-antigen-positive patients and appropriate controls were prepared using various sample preparation strategies including immunoenrichment, ultrafiltration, high-abundant protein depletion, deglycosylation, reverse-phase fractions, and digest using various enzymes. Samples were then analyzed by nanospray tandem mass spectrometry. Accurate mass TOF scans underwent molecular feature extraction and statistical analysis for unique disease makers, and acquired MS/MS data were searched against known human and histoplasma proteins. In human urine, some 52 peptides from 37 Histoplasma proteins were identified with high confidence. This is the first report of identification of a large number of Histoplasma-specific peptides from immunoassay-positive patient samples using tandem mass spectrometry and bioinformatics techniques. These findings may lead to novel diagnostic markers for histoplasmosis in human urine.

Disseminated histoplasmosis is an invasive fungal infection that can be fatal in patients with weak immune system. The goal of our exploratory study was to evaluate differences in urinary protein profiles among samples of healthy individuals, patients with proteinuria (PRU), and histoplasma antigenuria (HIS), and to identify physiological pathways associated with the excreted proteins. Urine samples were depleted of abundant proteins, deglycosylated, digested with trypsin, fractionated and analyzed by nano-LC-QTOF. The total number of human proteins identified in the samples was 117, of which 20 and 23 were unique to the samples from patients with PRU and HIS, respectively. Pathway analysis of proteins identified in samples of PRU and HIS patients suggested increased levels of proteins associated with acute response signaling, coagulation system, prothrombin activation, glucocorticoid regulation and the lipid antigen presentation signaling pathway networks. The obtained data provide information on protein expression associated with HIS, and suggest that further more rigorous studies aimed at the identification of proteins associated with proteinuria of different causes are feasible.

Background Serum thyroid stimulating hormone (TSH) measurements are useful for detecting clinical and subclinical primary hypo- and hyperthyroidism in ambulatory patients. For diagnosis of hyperthyroidism, the functional sensitivity (FS) is an important performance criterion, and current guidelines recommend an FS of ≤ 0.02 m IU/l for “third” generation performance. Methods We evaluated TSH FS for the Access 2, Advia Centaur, Architect i2000, Dimension ExL Modular Analytics E170, Immulite 2000 and Dimension Vista 1500 automated immunoassays using serum pools tested over a 6 week period using 2 reagent lots and 2 calibrations. FS was determined by fitting a power function to the imprecision data using KaleidaGraph software. Results The FS (m IU/l) for Access 2, ADVIA Centaur, ARCHITECT i2000, Dimension ExL, Modular Analytics E170, Immulite 2000, and Dimension Vista 1500 systems were determined to be 0.039, 0.006, 0.007, 0.003, 0.008, 0.003, and 0.003, respectively. The lowest and next to lowest pools had overall mean TSH concentrations of 0.012 m IU/l and 0.020 m IU/l, respectively and a range of concentrations of 0.005 to 0.022 m IU/l and 0.007 to 0.077 m IU/l, respectively. Conclusions All assays showed excellent performance in FS consistent with a “third” generation claim except for the Access 2 system. Further harmonization of TSH immunoassays is required, especially at lower concentrations.

Mass spectrometry is rapidly expanding its role in clinical chemistry. To date, this growth has primarily been in the area of small molecule analysis, though the field now seems set for a rapid growth of protein and peptide analysis. Small molecule analysis applications can be grouped roughly into the analysis of endogenous compounds and the analysis of exogenous compounds. The analysis of exogenous compounds is largely the domain of toxicology, and this is the focus of this article. To limit the scope and, therefore, the length of this article, we focus primarily on 2 general topics within clinical toxicology: therapeutic drug monitoring and trace element analysis. While these 2 topics do not cover the full breadth of mass spectrometry applications in clinical toxicology, omitting, for example, clinical drugsof-abuse testing and applications supporting poison control programs, we feel that they, nevertheless, provide a fairly representative overview of mass spectrometry in the clinical toxicology lab.

We developed a high sensitivity method for simultaneous measurement of cortisol, cortisone and dexamethasone. Using this method, we compared concentrations of cortisol, cortisone and their ratios in samples from intensive care unit (ICU) and non-ICU patients, and cortisol and dexamethasone concentrations in patients with Cushing's and suspected Cushing's syndrome.Two hundred microliters of human serum aliquots were extracted using solid phase extraction and analyzed using liquid chromatography-tandem mass spectrometry. Primary mass transitions monitored for cortisol, cortisone and dexamethasone were m/z 363/121, 361/163 and 393/373 respectively.The limits of quantification for cortisol and cortisone were 0.3 μg/l (0.8 nmol/l) and for dexamethasone it was 0.5 μg/l (1.2 nmol/l). Total imprecision was10.9%. Median cortisol to cortisone ratio of ICU patient samples was found to be 2 times higher than non-ICU samples. 54.2% of patients after 1mg dose of overnight dexamethasone could be categorized as consistent with Cushing's syndrome.The method has high sensitivity and specificity. High cortisol to cortisone ratios in samples from ICU patients suggest change in activity of 11β-hydroxysteroid dehydrogenase in modulation of systemically available cortisol. Simultaneous measurement of dexamethasone and cortisol can be used to differentially diagnose diseases causing increased concentrations of cortisol.

Liquid chromatography tandem mass spectrometry is one of the most specific techniques available in clinical laboratories. In the past, immunoassays were the primary methodology for analysis of steroids in biological samples because they are rapid and easy to perform. However, these methods were shown to suffer from the lack of specificity for measuring many of the diagnostically important steroids. LC-MS/MS overcomes many of the limitations of immunoassays, enhances diagnostic utility of the testing, and expands diagnostic capabilities in endocrinology. In addition to the superior quality of the measurements, LC-MS/MS allows high throughput testing using small sample volume with minimal sample preparation, and frees the laboratory from dependence on suppliers of assay specific reagents. LC-MS/MS is being widely employed for routine measurement of steroids, and the methodology plays an important role in the standardization and harmonization of measurements among clinical laboratories.

Objective To compare steroid concentrations and steroid product-to-precursor ratios in ovarian follicular fluid (FF) from women with polycystic ovary syndrome (PCOS) and from regularly menstruating women in their early follicular phase, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Polycystic ovary syndrome involves abnormal regulation of the steroidogenic enzymes, leading to arrest of follicle development. Design Case-control study. Setting University hospital clinic. Patient(s) Follicular fluid from size-matched ovarian follicles (5–8 mm) in 27 nonstimulated women with PCOS and in 21 women without PCOS was sampled. Thirteen steroids were quantitated from 40 μL of FF, using LC-MS/MS. Intervention(s) None. Main Outcome Measure(s) Concentrations of steroids in the FF and product-to-precursor ratios (enzyme activity) were compared between the groups. Result(s) In women with PCOS, ovarian FF contained higher concentrations of individual and total androgens, lower individual and total estrogens (E), and a lower total E-to-androgen ratio, compared with regularly menstruating women. The product-to-precursor concentration ratios indicated higher CYP17-linked and lower CYP19-linked (aromatase) enzyme activity. Receiver operating characteristic plots indicated the early CYP17 step (17-OH5P/5P) being highly important for the prevalence of PCOS (c = 0.95). Conclusion(s) The women with PCOS had higher ovarian CYP17-linked and lower CYP19-linked (aromatase) enzyme activity, confirming previous data. Multiple steroid assessments from minute volumes including FF from nonstimulated ovaries, using LC-MS/MS, might be useful in research, clinical endocrinology, and in IVF.

Measurement of 25-hydroxyvitamin D (25OH-vitD) is used to assess vitamin D status. We developed a high-sensitivity measurement method for 25OH-vitD and assessed the relationship between 25OH-vitD and parathyroid hormone (PTH) in healthy adults. Aliquots (100 microL) of serum were spiked with internal standard, proteins were precipitated, and samples were analyzed by liquid chromatography-tandem mass spectrometry using 2-dimensional chromatographic separation. Total imprecision was less than 10%, and the limit of quantitation was 1.0 ng/mL. We determined the distribution of concentrations of 25OH-vitD(2) and 25OH-vitD(3) in healthy adults using samples collected during winter and summer and evaluated the association between 25OH-vitD and PTH. The difference between median concentrations of 25OH-vitD in samples collected during winter and summer was 11 ng/mL (27 nmol/L). Statistically significant differences in concentrations of PTH were observed between groups of samples with 25OH-vitD less than 11 (27 nmol/L) and 11 to 15 ng/mL (27-37 nmol/L) and between groups with 25 to 30 (62-75 nmol/L) and more than 40 ng/mL (100 nmol/L). Among the advantages of this method are its high sensitivity and specificity.

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been recognized as a primary methodology for the accurate analysis of endogenous steroid hormones in biological samples. This review focuses on the use of LC-MS/MS in clinical laboratories to assist with the diagnosis of diverse groups of endocrine and metabolic diseases. Described analytical methods use on-line and off-line sample preparation and analytical derivatization to enhance analytical sensitivity, specificity, and clinical utility. Advantages of LC-MS/MS as an analytical technique include high specificity, possibility to simultaneously measure multiple analytes, and the ability to assess the specificity of the analysis in every sample. All described analytical methods were extensively validated, utilized in routine diagnostic practice, and were applied in a number of clinical and epidemiological studies, including a study of the steroidogenesis in ovarian follicles.

The majority of >2000 HLA class I molecules can be clustered according to overlapping peptide binding specificities or motifs recognized by CD8+ T cells. HLA class I motifs are classified based on the specificity of residues located in the P2 and the C-terminal positions of the peptide. However, it has been suggested that other positions might be relevant for peptide binding to HLA class I molecules and therefore be used for further characterization of HLA class I motifs. In this study we performed large-scale sequencing of endogenous peptides eluted from K562 cells (HLA class I null) made to express a single HLA molecule from HLA-B*3501, -B*3502, -B*3503, -B*3504, -B*3506, or -B*3508. Using sequence data from >1,000 peptides, we characterized novel peptide motifs that include dominant anchor residues extending to all positions in the peptide. The length distribution of HLA-B35-bound peptides included peptides of up to 15 residues. Remarkably, we determined that some peptides longer than 11 residues represented N-terminal-extended peptides containing an appropriate HLA-B35 peptide motif. These results provide evidence for the occurrence of endogenous N-terminal-extended peptide-HLA class I configurations. In addition, these results expand the knowledge about the identity of anchor positions in HLA class I-associated peptides that can be used for characterization of HLA class I motifs.

Background: The recent interest of clinical laboratories in developing serum testosterone assays based on isotope dilution–liquid chromatography–tandem mass spectrometry (ID-LC-MS/MS) stems from the lack of accuracy of direct immunoassays. In this study, we assessed the accuracy and state of standardization (traceability) of 4 published ID-LC-MS/MS procedures in a method comparison with an ID–gas chromatography (GC)–MS reference measurement procedure listed in the database of the Joint Committee for Traceability in Laboratory Medicine. Methods: The study used 58 specimens from different patient categories. Each specimen was measured in triplicate (ID-LC-MS/MS) and quadruplicate (ID-GC-MS) in independent runs. Results: The testosterone concentrations by ID-GC-MS were 0.2–4.4 nmol/L (women), 0.2–2.0 nmol/L (hypogonadal man), and 10.1–31.3 nmol/L (normogonadal men). For ID-GC-MS, the CV was nearly constant, with a median of 1.0%; for ID-LC-MS/MS, it was concentration-dependent, with a median of up to 8%. Weighted Deming regression gave mean slopes, intercepts, and correlation coefficients of 0.90–1.11, −0.055–0.013 nmol/L, and 0.993–0.997, respectively. The % difference plot showed between 7% and 26% of the results outside a total error limit of 14%, with median deviations from ID-GC-MS between −9.6 and 0.4%. Conclusions: This study demonstrated fairly good accuracy and standardization of the tested ID-LC-MS/MS procedures. Performance differences between procedures were evident in some instances, due to improper calibration and between-run calibration control. This emphasizes the need for thorough validation, including traceability, of new ID-LC-MS/MS procedures.