Measurement of 25-hydroxyvitamin D in the clinical laboratory: Current procedures, performance characteristics and limitations

In this review we describe procedures, performance characteristics and limitations of methods available for the measurement of 25-hydroxyvitamin (25OHD) since the year 2000. The two main types of methods are competitive immunoassay and those based on chromatographic separation followed by non-immunological direct detection (HPLC, LC-MS/MS). Lack of a reference standard for 25OHD has, until recently, been a major issue resulting in poor between-method comparability. Fortunately this should soon improve due to the recent introduction of a standard reference material in human serum (SRM 972) from the National Institute of Standards and Technology (NIST). For immunoassay, specificity can be an issue especially in relation to the proportion of 25OHD2 that is quantified whereas HPLC and LC-MS/MS methods are able to measure the two major vitamin D metabolites 25OHD2 and 25OHD3 independently. HPLC and LC-MS/MS require more expensive equipment and expert staff but this can be offset against lower reagent costs. Increasingly procedures are being developed to semi-automate or automate HPLC and LC-MS/MS but run times remain considerably longer than for immunoassays especially if performed on automated platforms. For most HPLC and LC-MS/MS methods extraction and procedural losses are corrected for by the inclusion of an internal standard which, in part, may account for higher results compared to immunoassay. In general precision of immunoassay, HPLC and LC-MS/MS are comparable and all have the required sensitivity to identify severe vitamin D deficiency. Looking to the future it is hoped that the imminent introduction of a standard reference method (or methods) for 25OHD will further accelerate improvements in between method comparability.     

Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification

Verification of candidate biomarker proteins in blood is typically done using multiple reaction monitoring (MRM) of peptides by LC-MS/MS on triple quadrupole MS systems. MRM assay development for each protein requires significant time and cost, much of which is likely to be of little value if the candidate biomarker is below the detection limit in blood or a false positive in the original discovery data. Here we present a new technology, accurate inclusion mass screening (AIMS), designed to provide a bridge from unbiased discovery to MS-based targeted assay development. Masses on the software inclusion list are monitored in each scan on the Orbitrap MS system, and MS/MS spectra for sequence confirmation are acquired only when a peptide from the list is detected with both the correct accurate mass and charge state. The AIMS experiment confirms that a given peptide (and thus the protein from which it is derived) is present in the plasma. Throughput of the method is sufficient to qualify up to a hundred proteins/week. The sensitivity of AIMS is similar to MRM on a triple quadrupole MS system using optimized sample preparation methods (low tens of ng/ml in plasma), and MS/MS data from the AIMS experiments on the Orbitrap can be directly used to configure MRM assays. The method was shown to be at least 4-fold more efficient at detecting peptides of interest than undirected LC-MS/MS experiments using the same instrumentation, and relative quantitation information can be obtained by AIMS in case versus control experiments. Detection by AIMS ensures that a quantitative MRM-based assay can be configured for that protein. The method has the potential to qualify large number of biomarker candidates based on their detection in plasma prior to committing to the time- and resource-intensive steps of establishing a quantitative assay.     

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures

LC-MS/MS has emerged as the method of choice for the identification and quantification of protein sample mixtures. For very complex samples such as complete proteomes, the most commonly used LC-MS/MS method, data-dependent acquisition (DDA) precursor selection, is of limited utility. The limited scan speed of current mass spectrometers along with the highly redundant selection of the most intense precursor ions generates a bias in the pool of identified proteins toward those of higher abundance. A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented. In the first stage of the strategy, all detectable peptide ion signals are extracted from high resolution LC-MS feature maps or aligned sets of feature maps. The selected features or a subset thereof are subsequently sequenced in sequential, non-redundant directed LC-MS/MS experiments, and the MS/MS data are mapped back to the original LC-MS feature map in a fully automated manner. The strategy, implemented on an LTQ-FT MS platform, allowed the specific sequencing of 2,000 features per analysis and enabled the identification of more than 1,600 phosphorylation sites using a single reversed phase separation dimension without the need for time-consuming prefractionation steps. Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions.     

Comparison of radioimmunoassay and liquid chromatography tandem mass spectrometry for determination of juvenile hormone titers

This paper compares the results of juvenile hormone (JH) titer determinations in two insect species, Melanoplus sanguinipes, a migratory grasshopper, and Acyrthosiphon pisum, the pea aphid, using a chiral-specific JH radioimmunoassay (RIA) and liquid chromatography tandem mass spectrometry (LC-MS/MS), after extraction of JH with either hexane or isooctane-methanol. We compared results of JH titer determinations done on extracts of M. sanguinipes hemolymph taken from animals flown to exhaustion in tethered flight tests or unflown controls and from whole body extracts of A. pisum raised at two different temperatures. In each case the two different treatments experienced by the experimental animals were expected to result in widely differing JH titers. Methoprene and precocene II were used as internal standards. Samples were split and titers determined simultaneously with both the LC-MS/MS and RIA procedures. Unambiguous detection of JH III by LC-MS/MS was done by identification of its specific parent ion and its mass fingerprint (m/z 289, 267, 249, 235, 217, and 189). We conclude that isooctane-methanol-extracted JH samples can be accurately analyzed by LC-MS/MS, but not by RIA without further separation of JH from contaminating lipids. Hexane extracted JH samples from hemolymph can be analyzed accurately by both RIA and LC-MS/MS. However, the RIA results from whole body extracts of aphids reared at two different temperatures were initially obscured with excess lipids even when hexane was the extraction solvent. Thus samples were further purified by Waters Sep-Pak C18 column, but contaminating phospholipids continued to cause problems with the RIA assay. The detection limit of JH III standard for RIA was 13.75+/-2.39 pg whereas that for LC-M/MS was 8.25+/-1.44 pg in our experimental conditions.     

Liquid chromatography-mass spectrometry/mass spectrometry method development for drug metabolism studies: Examining lipid matrix ionization effects in plasma

Glycerophosphocholines (GPCho's) are known to cause liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) matrix ionization effects during the analysis of biological samples (i.e. blood, plasma). We have developed a convenient new method, which we refer to as "in-source multiple reaction monitoring" (IS-MRM), for detecting GPCho's during LC-MS/MS method development. The approach uses high energy in-source collisionally induced dissociation (CID) to yield trimethylammonium-ethyl phosphate ions (m/z 184), which are formed from mono- and disubstituted GPCho's. The resulting ion is selected by the first quadrupole (Q1), passed through the collision cell (Q2) in the presence of collision gas at low energy to minimize fragmentation, and m/z 184 selected by the third quadrupole. This approach can be combined with standard multiple reaction monitoring (MRM) transitions with little compromise in sensitivity during method development and sample analysis. Hence, this approach was used to probe ionization matrix effects in plasma samples. The resulting information was employed to develop LC-MS/MS analyses for drugs and their metabolites with cycle times less than 5 min.     

LC-MS/MS in the Clinical Laboratory – Where to From Here?

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has seen enormous growth in clinical laboratories during the last 10-15 years. It offers analytical specificity superior to that of immunoassays or conventional high performance/pressure liquid chromatography (HPLC) for low molecular weight analytes and has higher throughput than gas chromatography-mass spectrometry (GC-MS). Drug/Toxicology and Biochemical Genetics/Newborn Screening laboratories were at the vanguard of clinical LC-MS/MS use, but have been eclipsed by Endocrine laboratories. In USA reference/referral laboratories, most steroids and biogenic amines are now assayed by LC-MS/MS, and the technology has started to penetrate into smaller laboratories. Assays for mineralo- and gluco-corticoids and their precursors, sex steroids, metanephrines and 25-hydroxy vitamin D highlight the advantages of LC-MS/MS.However, several limitations of LC-MS/MS have become apparent, centring on the interacting triangle of sensitivity - specificity - throughput. While sample throughput is higher than for conventional HPLC or GC-MS, it lags behind automated immunoassays. Techniques which improve throughput include direct sample injection, LC-multiplexing and samplemultiplexing. Measures to improve specificity and sensitivity include sample clean-up and optimising chromatography to avoid interferences and ion suppression due to sample-matrix components. Next generation instrumentation may offer additional benefits.The next challenge for clinical LC-MS/MS is peptide/protein analysis. The quest for multi-biomarker profiles for various diseases has largely failed, but targeted peptide and protein testing by LC-MS/MS, directed at analytical and clinical questions that need to be answered, is proving highly successful. We anticipate that this will result in similar growth of clinical protein/peptide LC-MS/MS as has been seen for low molecular weight applications.     

LC-MS based serum metabonomic analysis for renal cell carcinoma diagnosis, staging, and biomarker discovery

A LC-MS based method, which utilizes both reversed-performance (RP) chromatography and hydrophilic interaction chromatography (HILIC) separations, has been carried out in conjunction with multivariate data analysis to discriminate the global serum profiles of renal cell carcinoma (RCC) patients and healthy controls. The HILIC was found necessary for a comprehensive serum metabonomic profiling as well as RP separation. The feasibility of using serum metabonomics for the diagnosis and staging of RCC has been evaluated. One-hundred percent sensitivity in detection has been achieved, and a satisfactory clustering between the early stage and advanced-stage patients is observed. The results suggest that the combination of LC-MS analysis with multivariate statistical analysis can be used for RCC diagnosis and has potential in the staging of RCC. The MS/MS experiments have been carried out to identify the biomarker patterns that made great contribution to the discrimination. As a result, 30 potential biomarkers for RCC are identified. It is possible that the current biomarker patterns are not unique to RCC but just the result of any malignancy disease. To further elucidate the pathophysiology of RCC, related metabolic pathways have been studied. RCC is found to be closely related to disturbed phospholipid catabolism, sphingolipid metabolism, phenylalanine metabolism, tryptophan metabolism, fatty acid beta-oxidation, cholesterol metabolism, and arachidonic acid metabolism.     

Mining phosphopeptide signals in liquid chromatography-mass spectrometry data for protein phosphorylation analysis

Protein phosphorylation is a key post-translational modification that governs biological processes. Despite the fact that a number of analytical strategies have been exploited for the characterization of protein phosphorylation, the identification of protein phosphorylation sites is still challenging. We proposed here an alternative approach to mine phosphopeptide signals generated from a mixture of proteins when liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis is involved. The approach combined dephosphorylation reaction, accurate mass measurements from a quadrupole/time-of-flight mass spectrometer, and a computing algorithm to differentiate possible phosphopeptide signals obtained from the LC-MS analyses by taking advantage of the mass shift generated by alkaline phosphatase treatment. The retention times and m/z values of these selected LC-MS signals were used to facilitate subsequent LC-MS/MS experiments for phosphorylation site determination. Unlike commonly used neutral loss scan experiments for phosphopeptide detection, this strategy may not bias against tyrosine-phosphorylated peptides. We have demonstrated the applicability of this strategy to sequence more, in comparison with conventional data-dependent LC-MS/MS experiments, phosphopeptides in a mixture of alpha- and beta-caseins. The analytical scheme was applied to characterize the nasopharyngeal carcinoma (NPC) cellular phosphoproteome and yielded 221 distinct phosphorylation sites. Our data presented in this paper demonstrated the merits of computation in mining phosphopeptide signals from a complex mass spectrometric data set.     

Halogenated Peptides as Internal Standards (H-PINS): INTRODUCTION OF AN MS-BASED INTERNAL STANDARD SET FOR LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY*

As the application for quantitative proteomics in the life sciences has grown in recent years, so has the need for more robust and generally applicable methods for quality control and calibration. The reliability of quantitative proteomics is tightly linked to the reproducibility and stability of the analytical platforms, which are typically multicomponent (e.g. sample preparation, multistep separations, and mass spectrometry) with individual components contributing unequally to the overall system reproducibility. Variations in quantitative accuracy are thus inevitable, and quality control and calibration become essential for the assessment of the quality of the analyses themselves. Toward this end, the use of internal standards cannot only assist in the detection and removal of outlier data acquired by an irreproducible system (quality control) but can also be used for detection of changes in instruments for their subsequent performance and calibration. Here we introduce a set of halogenated peptides as internal standards. The peptides are custom designed to have properties suitable for various quality control assessments, data calibration, and normalization processes. The unique isotope distribution of halogenated peptides makes their mass spectral detection easy and unambiguous when spiked into complex peptide mixtures. In addition, they were designed to elute sequentially over an entire aqueous to organic LC gradient and to have m/z values within the commonly scanned mass range (300–1800 Da). In a series of experiments in which these peptides were spiked into an enriched N-glycosite peptide fraction (i.e. from formerly N-glycosylated intact proteins in their deglycosylated form) isolated from human plasma, we show the utility and performance of these halogenated peptides for sample preparation and LC injection quality control as well as for retention time and mass calibration. Further use of the peptides for signal intensity normalization and retention time synchronization for selected reaction monitoring experiments is also demonstrated.As proteomics and systems biology converge, the need for the generation of high quality, large scale quantitative proteomics data sets has grown, and so-called label-free quantification has emerged as a very useful platform for their generation (1). Label-free quantitative experiments are usually designed to detect differentially abundant features in biologically relevant samples by comparing mass versus retention time feature maps generated by LC-MS. Although label-free proteomics experiments are time- and cost-effective, they require high levels of reproducibility at every step of the process (2). Too much variation resulting from sample preparation, LC performance (e.g. injection, gradient delivery, and flow rate), and MS performance (e.g. ionization efficiency, mass accuracy, and detector performance) could lead to an increase in the false discovery rate of detected peptides. Thus it is crucial to minimize such variation to adequately control the quality of the data. In addition, label-free experiments are often followed by directed MS/MS analyses in which selected peptides are specifically targeted for identification, a procedure that also requires high system reproducibility (3, 4). The total variation in the acquired data is the result of accumulating variation at each step. This variation, regardless of its source, be it from sample handling, injection irreproducibility, change in analyte volume, matrix and co-eluter interference (both suppression and enhancement), system instability, or finally variations in the ion source performance, can be accounted for if an appropriate internal standard (ISTD)¹ system is used.A more recent development in the field of quantitative proteomics is multireaction monitoring (MRM) also referred to as selected reaction monitoring (SRM). This MS-based technology is aimed at fast, sensitive, and reproducible screening of large sets of known targets and is ideal for building biological assays in which the presence and quantity of specific analytes is being determined in multiple samples. Certain inputs, such as transitional values (m/z values for the precursor ion and its fragment ions), collision energies, and chromatographic retention time are required to build a validated S/MRM assay. These values are either extracted from MS/MS data acquired from biological samples with the same type of instrument used for the S/MRM analyses or from a set of peptide standards (5). To maximize the number of S/MRM measurements in one LC-MS/MS run, the use of elution time constraints has proven to be highly beneficial (6). ISTDs could therefore play an integral role in building S/MRM assays if used to synchronize input values such as retention times between instruments or to monitor the retention time consistency in sequences of scheduled S/MRM experiments.ISTDs are usually designed to best fit the analytical system for which they are being used. Because the currency of quantitative proteomics is ionized peptide ions, peptides thus represent the best candidates for ISTDs for proteomics measurements. The use of peptides as ISTDs for proteomics applications, however, is not new. Both natural peptides and heavy isotope-labeled peptides (either chemically synthesized or produced by tryptic digestion of biologically expressed quantification concatamers (QconCATs)) have been used as internal standards by spiking (7, 8). Peptides from the biological analyte have also been used as pseudo-internal standards for normalization (9). But a limitation with all these methods that use native and heavy isotope-labeled peptides as ISTDs is signal detection. The MS-based signal detection for this type of peptide can be challenging when trying to confidently detect their signal in ion chromatograms acquired by mass spectral analysis of biological fluids or other samples of similar complexity where densely packed features cover the entire mass and time range (10). In addition, there is always a chance that a peptide with the same elemental composition as the internal standard might exist in the analyte and thus completely throw off the calibration curve (11). The same argument is valid for heavy isotope-labeled peptides because in many quantitative applications the analytical matrix is made of heavy isotope-labeled peptides (12–14). Obviously utilization of ISTDs in complex mixtures requires highly confident detection of corresponding signals, and for natural and heavy isotope-labeled peptides MS/MS analysis is the only way to accomplish that. But CID attempts on mass spectral features do not necessarily result in identification. First the MS features from ISTDs have to be picked for CID, and then the fragmentation should result in high quality MS/MS spectra that could be matched to the ISTD sequence with high confidence. This process is not always successful and consequently can result in an incomplete set of ISTD signals. The other limitation of MS/MS-based ISTDs is processing time. All MS/MS data have to be searched and curated before ISTD signals can be used.On the other hand, if ISTD signals could be easily detected at the MS level, then all the aforementioned limitations are lifted. For such a peptide to be an MS-based ISTD, it should really have unusual properties that make it easily detectable in a background of biological peptides.In this study we introduce the use of a set of halogenated peptides as internal standards (H-PINS) with unique isotopic distributions and mass defect that are easily detectable at the MS level by manual search and automated peak picking algorithms. The pattern of the isotopic distribution and mass defect are essential for detection of H-PINS at the MS level. Hence these peptides are best suited for high resolution and mass accuracy instruments. These peptides are similar to ordinary peptides in any other respect and can be treated similarly during purification and LC-MS analysis. We go on to illustrate their use for quality control (QC) at various steps of a proteomics experiment including sample preparation, LC-MS, and mass calibration and retention time synchronization between various analytical platforms.     

LC-MS/MS detection of peroxynitrite-derived 3-nitrotyrosine in rat microvessels

3-Nitrotyrosine (3NT) is used as a biomarker of nitrative pathology caused by peroxynitrite (PN), myeloperoxidase (MPO)-, and/or eosinophil peroxidase (EPO)-dependent nitrite oxidation. 3NT measurements in biological materials are usually based on either antibody staining, HPLC detection, or GC detection methodologies. In this report, a procedure is described for the measurement of 3NT and tyrosine (TYR) by LC-MS/MS that is simple, direct, and sensitive. Though highly specialized in its use as an assay, LC-MS/MS technology is available in many research centers in academia and industry. The critical assay for 3NT was linear below 100 ng/ml and the limit of detection was below 100 pg/ml. Regarding protein digested samples, we found that MRM was most selective with 133.1 m/z as the daughter ion. In comparison, LC-ECD was 100 times less sensitive. Basal levels of 3NT in extracted digests of rat brain homogenate were easily detected by LC-MS/MS, but were below detection by LC-ECD. The LC-MS/MS assay was used to detect 3NT in rat brain homogenate that was filtered through a 180 micron nylon mesh. Three fractions were collected and examined by phase contrast microscopy. The mass ratio (3NT/TYR) of 3NT in fractions of large vessel enrichment, microvessel enrichment, and vessel depletion was 0.6 ng/mg, 1.2 ng/mg, and 0.2 ng/mg, respectively. Ultimately, we found that the basal 3NT/TYR mass ratio as determined by LC-MS/MS was six times greater in microvessel-enriched brain tissue vs. tissue devoid of microvessels.     

Tube-gel digestion: a novel proteomic approach for high throughput analysis of membrane proteins

This study describes a new protein digestion protocol in which a variety of detergents can be used to solubilize membrane proteins and facilitate trypsin digestion with higher efficiency. In this protocol, proteins are dissolved in solutions containing various detergents and directly incorporated into a polyacrylamide gel matrix without electrophoresis. Detergents are subsequently eliminated from the gel matrix while proteins are still immobilized in the gel matrix. After in-gel digestion of proteins, LC-MS/MS is used to analyze the extracted peptides for protein identification. The uniqueness of the protocol is that it allows usage of a variety of detergents in the starting solution without interfering with LC-MS/MS analysis. We hereby demonstrate that different detergents, including ionic SDS, non-ionic Triton X-100 and n-octyl beta-d-glucopyranoside, and zwitterionic CHAPS, can be used to achieve maximum solubilization of membrane proteins with minimal interference with LC-MS/MS analysis. Enhanced digestions, i.e. improved number and intensity of detected peptides, are also demonstrated for digestion-resistant proteins such as myoglobin, ubiquitin, and bacteriorhodopsin. An additional advantage of the Tube-Gel digestion protocol is that, even without electrophoresis separation, it allows high throughput analysis of complex protein mixtures when coupled with LC-MS/MS. The protocol was used to analyze a complex membrane protein mixture prepared from prostate cancer cells. The protocol involves only a single digestion and 2.5 h of LC-MS/MS analysis and identified 178 membrane proteins. In comparison, the same membrane fraction was resolved by SDS-PAGE, and 20 gel slices were excised and individually digested and analyzed by LC-MS/MS. The more elaborate effort demanded more than 50 h of LC-MS/MS analysis and identified 268 proteins. The new Tube-Gel digestion protocol is an alternative method for high throughput analysis of membrane proteins.     

Increase of the LC-MS/MS sensitivity and detection limits using on-line sample preparation with large volume plasma injection

Large volume injection (LVI) has systematically been studied to improve LC-MS/MS sensitivity (signal-to-noise ratio, or S/N) and detection limits. The method of LVI was combined with on-line solid phase extraction (on-line SPE) and LC-MS/MS detection for analysis of compounds directly in plasma. It was demonstrated that LVI of plasma with on-line SPE-LC-MS/MS allows for improvement of sensitivity and detection limits without compromising chromatographic peak shape and resolution and inducing significant matrix and signal suppression effects. Furthermore, sensitivity and detection limits improve linearly with the injection volume up to 100 microL. Quantification of the model compounds in plasma demonstrated comparable calibration curve statistics, precision and accuracy for 5, 50 and 100 microL plasma injections.     

Development of an on-line extraction turbulent flow chromatography tandem mass spectrometry method for cassette analysis of Caco-2 cell based bi-directional assay samples

Caco-2 cells are frequently used for screening compounds for their permeability characteristics and P-glycoprotein (P-gp) interaction potential. Bi-directional permeability studies performed on Caco-2 cells followed by analysis by HPLC-UV or LC-MS method constitutes the "method of choice" for the functional assessment of efflux characteristics of a test compound. A high throughput LC-MS/MS method has been developed using on-line extraction turbulent flow chromatography coupled to tandem mass spectrometric detection to analyze multiple compounds present in Hanks balanced salt solution in a single analytical run. All standard curves (P-gp substrates: quinidine, etoposide, rhodamine 123, dexamethasone, and verapamil and non-substrates: metoprolol, sulfasalazine, propranolol, nadolol, and furosemide) were prepared in a cassette mode (ten-in-one) while Caco-2 cell incubations were performed both in discreet mode and in cassette mode. The standard curve range for most compounds was 10-2500 nM with regression coefficients (R(2)) greater than 0.99 for all compounds. The applicability and reliability of the analysis method was evaluated by successful demonstration of efflux ratio greater than 1 for the P-gp substrates studied in the Caco-2 cell model. The use of cassette mode analysis through selected reaction monitoring mass spectrometry presents an attractive option to increase the throughput, sensitivity, selectivity, and efficiency of the model over discreet mode UV detection.     

Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.LC-MS/MS provides the most widely used technology platform for proteomics analyses of purified proteins, simple mixtures, and complex proteomes. In a typical analysis, protein mixtures are proteolytically digested, the peptide digest is fractionated, and the resulting peptide fractions then are analyzed by LC-MS/MS (1, 2). Database searches of the MS/MS spectra yield peptide identifications and, by inference and assembly, protein identifications. Depending on protein sample load and the extent of peptide fractionation used, LC-MS/MS analytical systems can generate from hundreds to thousands of peptide and protein identifications (3). Many variations of LC-MS/MS analytical platforms have been described, and the performance of these systems is influenced by a number of experimental design factors (4).Comparison of data sets obtained by LC-MS/MS analyses provides a means to evaluate the proteomic basis for biologically significant states or phenotypes. For example, data-dependent LC-MS/MS analyses of tumor and normal tissues enabled unbiased discovery of proteins whose expression is enhanced in cancer (5–7). Comparison of data-dependent LC-MS/MS data sets from phosphotyrosine peptides in drug-responsive and -resistant cell lines identified differentially regulated phosphoprotein signaling networks (8, 9). Similarly, activity-based probes and data-dependent LC-MS/MS analysis were used to identify differentially regulated enzymes in normal and tumor tissues (10). All of these approaches assume that the observed differences reflect differences in the proteomic composition of the samples analyzed rather than analytical system variability. The validity of this assumption is difficult to assess because of a lack of objective criteria to assess analytical system performance.The problem of variability poses three practical questions for analysts using LC-MS/MS proteomics platforms. First, is the analytical system performing optimally for the reproducible analysis of complex proteomes? Second, can the sources of suboptimal performance and variability be identified, and can the impact of changes or improvements be evaluated? Third, can system performance metrics provide documentation to support the assessment of proteomic differences between biologically interesting samples?Currently, the most commonly used measure of variability in LC-MS/MS proteomics analyses is the number of confident peptide identifications (11–13). Although consistency in numbers of identifications may indicate repeatability, the numbers do not indicate whether system performance is optimal or which components require optimization. One well characterized source of variability in peptide identifications is the automated sampling of peptide ion signals for acquisition of MS/MS spectra by instrument control software, which results in stochastic sampling of lower abundance peptides (14). Variability certainly also arises from sample preparation methods (e.g. protein extraction and digestion). A largely unexplored source of variability is the performance of the core LC-MS/MS analytical system, which includes the LC system, the MS instrument, and system software. The configuration, tuning, and operation of these system components govern sample injection, chromatography, electrospray ionization, MS signal detection, and sampling for MS/MS analysis. These characteristics all are subject to manipulation by the operator and thus provide means to optimize system performance.Here we describe the development of 46 metrics for evaluating the performance of LC-MS/MS system components. We have implemented a freely available software pipeline that generates these metrics directly from LC-MS/MS data files. We demonstrate their use in characterizing sources of variability in proteomics platforms, both for replicate analyses on a single instrument and in the context of large interlaboratory studies conducted by the National Cancer Institute-supported Clinical Proteomic Technology Assessment for Cancer (CPTAC)1 Network.     

Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry

Protein cleavage-isotope dilution mass spectrometry (PC-IDMS) can be used to quantify proteins, with an isotope-labeled analogue of the peptide fragment used as an internal standard. Here, we investigate use of a standard LC-MS/MS platform for quantifying a model biomarker directly from serum by this technique. We synthesized a peptide (IVGGWECEK) identical to the N-terminal tryptic fragment of PSA but with each glycine containing two 13C atoms and one 15N atom. PSA-free human serum was denatured with urea followed by the introduction of PSA standard and the stable isotope labeled internal standard peptide. The sample was then proteolyzed with trypsin and subjected to quantification using LC-MS/ MS on a triple quadrupole mass spectrometer. A linear least squares calibration curve made from five different concentrations of PSA added to serum and digested (each made in triplicate and randomly injected three times) had a mean slope of 0.973 (SE = 0.023), intercept of -0.003 (SE = 0.022), and R2 of 0.971. Recovery of calibrators ranged from 70 to 85% with a mean run-to-run CV of 13% and a mean within-run CV of 5.7%. PC-IDMS is a promising technique for quantifying proteins covering a broad range of applications from standardizing immunoassays to monitoring post-translational modifications to quantifying newly discovered biomarkers prior to the development and implementation of an immunoassay, just to name a few. Issues surrounding the application of PC-IDMS for the absolute quantification of proteins include selection of a proteolytic fragment for quantification that can be cleaved and isolated reproducibly over a broad dynamic range, stable isotope labeled synthetic peptide standards that give consistent results, and LC-MS/MS methods that provide adequate sensitivity and reproducibility without creating impractical analysis times. The results presented here show that absolute quantification can be performed on the model biomarker PSA introduced into denatured serum when analyzed by LC-MS/MS. However, concerns still exist regarding sensitivity compared to existing immunoassays as well as the reproducibility of PC-IDMS performed in different matrixes.     

MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics

MOTIVATION: Mass spectrometry (MS) data are impaired by noise similar to many other analytical methods. Therefore, proteomics requires statistical approaches to determine the reliability of regulatory information if protein quantification is based on ion intensities observed in MS. RESULTS: We suggest a procedure to model instrument and workflow-specific noise behaviour of iTRAQ reporter ions that can provide regulatory information during automated peptide sequencing by LC-MS/MS. The established mathematical model representatively predicts possible variations of iTRAQ reporter ions in an MS data-dependent manner. The model can be utilized to calculate the robustness of regulatory information systematically at the peptide level in so-called bottom-up proteome approaches. It allows to determine the best fitting regulation factor and in addition to calculate the probability of alternative regulations. The result can be visualized as likelihood curves summarizing both the quantity and quality of regulatory information. Likelihood curves basically can be calculated from all peptides belonging to different regions of proteins if they are detected in LC-MS/MS experiments. Therefore, this approach renders excellent opportunities to detect and statistically validate dynamic post-translational modifications usually affecting only particular regions of the whole protein. The detection of known phosphorylation events at protein kinases served as a first proof of concept in this study and underscores the potential for noise models in quantitative proteomics.     

Performance metrics for evaluating system suitability in liquid chromatography—Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

The use of liquid chromatography – mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS² acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS.     

MSSimulator: Simulation of mass spectrometry data

Mass spectrometry coupled to liquid chromatography (LC-MS and LC-MS/MS) is commonly used to analyze the protein content of biological samples in large scale studies, enabling quantitation and identification of proteins and peptides using a wide range of experimental protocols, algorithms, and statistical models to analyze the data. Currently it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists for peptide identification algorithms but data that represents a ground truth for the evaluation of LC-MS data is limited. Hence there have been attempts to simulate such data in a controlled fashion to evaluate and compare algorithms. We present MSSimulator, a simulation software for LC-MS and LC-MS/MS experiments. Starting from a list of proteins from a FASTA file, the simulation will perform in-silico digestion, retention time prediction, ionization filtering, and raw signal simulation (including MS/MS), while providing many options to change the properties of the resulting data like elution profile shape, resolution and sampling rate. Several protocols for SILAC, iTRAQ or MS(E) are available, in addition to the usual label-free approach, making MSSimulator the most comprehensive simulator for LC-MS and LC-MS/MS data.     

A systematical analysis of tryptic peptide identification with reverse phase liquid chromatography and electrospray ion trap mass spectrometry

In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identified peptides in reverse phase liquid chromatography and electrospray tandem mass spectrometry (RPLC-MS/MS) analysis. Following protein digestion with trypsin, the peptide mixture was analyzed by on-line RPLC-MS/MS. Bovine serum albumin (BSA) was used to optimize acetonitrile (ACN) elution gradient for tryptic peptides, and Cytochrome C was used to retest the gradient and the sensitivity of LC-MS/MS. The characteristics of identified peptides were also analyzed. In our experiments, the suitable ACN gradient is 5% to 30% for tryptic peptide elution and the sensitivity of LC-MS/MS is 50 fmol.Analysis of the tryptic peptides demonstrated that longer (more than 10 amino acids) and multi-charge state ( 2, 3) peptides are likely to be identified, and the hydropathicity of the peptides might not be related to whether it is more likely to be identified or not. The number of identified peptides for a protein might be used to estimate its loading amount under the same sample background. Moreover, in this study the identified peptides present three types of redundancy, namely identification, charge, and sequence redundancy, which may repress low abundance protein identification.     

Comparison of 2-D LC and 3-D LC with post- and pre-tryptic-digestion SEC fractionation for proteome analysis of normal human liver tissue

The current "shotgun" proteomic analysis, strong cation exchange-RPLC-MS/MS system, is a widely used method for proteome research. Currently, it is not suitable for complicated protein sample analysis, like mammal tissues or cells. To increase the protein identification confidence and number, an additional separation dimension for sample fractionation is necessary to be coupled prior to current multi-dimensional protein identification technology (MudPIT). In this work, SEC was elaborately selected and applied for sample prefractionation in consideration of its non-bias against sample and variety of choice of mobile phases. The analysis of the global lysate of normal human liver tissue sample provided by the China Human Liver Proteome Project, were performed to compare the proteome coverage, sequence coverage (peptide per protein identification) and protein identification efficiency in MudPIT, 3-D LC-MS/MS identification strategy with preproteolytic and postproteolytic fractionation. It was demonstrated that 3-D LC-MS/MS utilizing protein level fractionation was the most effective method. A MASCOT search using the MS/MS results acquired by QSTAR(XL) identified 1622 proteins from 3-D LC-MS/MS identification approaches. A primary analysis on molecular weight, pI and grand average hydrophobicity value distribution of the identified proteins in different approaches was made to further evaluate the 3-D LC-MS/MS analysis strategy.