Evaluation of dimethyl sulfoxide (DMSO) as a mobile phase additive during top 3 label-free quantitative proteomics

Acetic acid is a superior ion pairing modifier for sub-nanogram and single cell proteomics

A recent study demonstrated a substantial increase in peptide signal and corresponding proteome coverage when employing 0.5% acetic acid (AA) as the ion pairing modifier in place of the 0.1% formic acid traditionally used in shotgun proteomics. In this study, we investigated the effect of modifier in the context of sub-nanogram and single cell proteomics (SCP). We first evaluated a tryptic digest standard down to 20 picograms total load on column on a TIMSTOF SCP system. In line with the previous results, we observed a signal increase when using AA, leading to increased proteome coverage at every peptide load assessed. Relative improvements were more apparent at lower concentrations, with a 20 picogram peptide digest demonstrating a striking 1.8-fold increase to over 2,000 protein groups identified in a 30 minute analysis. Furthermore, we find that this increase in signal can be leveraged to reduce ramp times, leading to 1.7x more scans across each peak and improvements in quantification as measured by %CVs. When evaluating single cancer cells, approximately 13% more peptide groups were identified on average when employing AA in the place of FA. All vendor raw and processed data are available through ProteomeXchange as PXD046002 and PXD051590.

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Dimethyl sulfoxide as a gas phase charge-reducing agent for the determination of PEGylated proteins' intact mass

Determination of PEGylated proteins' intact mass by mass spectrometry is challenging due to the molecules' large size, excessive charges, and instrument limitations. Previous efforts have been reported. However, signal variability, ion coalescence, and a generally low degree of robustness have been observed. In this work, we have explored the capabilities of post-column infusion of dimethyl sulfoxide (DMSO) following reversed-phase liquid chromatography-mass spectrometry (RP-LCMS) to determine PEG-filgrastim' intact mass, and to characterize its PEG moiety. The method was optimized around reproducibility (six preparations, and three injection replicates) with an in-house prepared PEG-filgrastim standard. The method showed a mass accuracy of ≤1.2 Da. The average molecular weight (MWEO=483) was 40 147.9 Da. The number average molecular weight (Mn) and the weight average molecular weight (Mw) were observed to be 40 101.1 and 40 113.9 Da, respectively, both with an RSD of 0.03%. The molecular weight distribution of ethylene oxide (EO), the polydispersity index (PDI), was 1.0003 for all preparations with a minimum and maximum number of EO units of 448 ± 2 and 516 ± 2, respectively. The method was finally applied to commercially available Neulasta® lots where the Mn and Mw were 39 995.8 and 40 008.8 Da, respectively, both with an RSD of 0.1%. The minimum and maximum EO units across the lots were observed to be 444.5 ± 1.5 and 514 ± 3, respectively. The PDI for all Neulasta® lots was 1.0003. This study provides an insightful characterization of Neulasta® and describes a robust LC-MS methodology for the characterization of the PEGylated proteins.

Investigational Study of DASATINIB N-Oxide Impurity in Different Diluents

Dasatinib is an aminopyrimidine used as an inhibitor of multiple tyrosine kinases in two different formulations an immediate-release tablet and a powder for oral suspension. It shows a very low pH-dependent solubility in aqueous solutions and higher solubility in organic solvents. The solubility plays an essential role in analytical methodology to establish the purity, potency, safety and efficacy of any drug product as a diluent. Also, extraction of active drug substance with a suitable diluent from matrix composition is crucial for any analytical method development. However, a diluent optimization study during the method development of related substances for the drug product reveals that the Piperazine ring presented in Dasatinib is susceptible to oxidation and forms an N-oxide impurity. The impurity formation is due to the micro oxidic properties of the solvent used as a diluent which is inducing an oxidation reaction. Therefore, a comprehensive investigative study was conducted to optimize the diluent by limiting N-Oxide generation.

The Finding of New In Vivo Metabolite Triptorelin (5-10) in Human Urine Using Liquid Chromatography Coupled with Ion Trap/Time-of-Flight Mass Spectrometry with Dimethyl Sulfoxide Additives in the Mobile Phase

Triptorelin and leuprorelin are synthetic gonadotrophin-releasing hormones (GnRH) that are on the World Anti-Doping Agency (WADA) list of prohibited substances. To investigate the possible in vivo metabolites of triptorelin and leuprorelin in humans compared to previously reported in vitro metabolites, excreted urine from five patients treated with either triptorelin or leuprorelin was analyzed by liquid chromatography coupled with ion trap/time-of-flight mass spectrometry (LC/MS-IT-TOF). The addition of dimethyl sulfoxide (DMSO) to the mobile phase was found to enhance the detection sensitivity of certain GnRH analogs. The method was validated, and the limit of detection (LOD) was found at 0.02-0.08 ng/mL. Using this method, a novel new metabolite of triptorelin was discovered in the urine of all subjects up to 1 month after triptorelin administration, but it was not observed in the urine of subjects before drug administration. The limit of detection was estimated to be 0.05 ng/mL. The structure of the metabolite, triptorelin (5-10), is proposed from bottom-up mass spectrometry analysis. The discovery of in vivo triptorelin (5-10) can possibly be used as supporting evidence of triptorelin misuse in athletes.

A distributable LC-MS/MS method for the measurement of serum thyroglobulin

Background

Despite its clear advantages over immunoassay-based testing, the measurement of serum thyroglobulin by mass spectrometry remains limited to a handful of institutions. Slow adoption by clinical laboratories could reflect limited accessibility to existing methods that have sensitivity comparable to modern immunoassays, as well as a lack of tools for calibration and assay harmonization.

Methods

We developed and validated a liquid chromatography-tandem mass spectrometry-based assay for the quantification of serum thyroglobulin. The protocol combined peptide immunoaffinity purification using a commercially available, well-characterized monoclonal antibody and mobile phase modification with dimethylsulfoxide (DMSO) for enhanced sensitivity. To facilitate harmonization with other laboratories, we developed a novel, serum-based 5-point distributable reference material (Husky Ref).

Results

The assay demonstrated a lower limit of quantification of 0.15 ng/mL (<20 %CV). Mobile phase DMSO increased signal intensity of the target peptide at least 3-fold, improving quantification at low concentrations. Calibration traceable to Husky Ref enabled harmonization between laboratories in an interlaboratory study.

Conclusions

Sensitive mass spectrometry-based thyroglobulin measurement can be achieved using a monoclonal antibody during peptide immunoaffinity purification and the addition of mobile phase DMSO. Laboratories interested in deploying this assay can utilize the provided standard operating procedure and freely-available Husky Ref reference material.

Combining direct urinary injection with automated filtration and nanoflow LC-MS for the confirmatory analysis of doping-relevant small peptide hormones

Nano-liquid chromatography (nanoLC) has proven itself as a powerful tool and its scope entails various applications in (bio)analytical fields. Operation at low (nL/min) flow rates in combination with reduced inner dimensions (ID < 100 µm), leads to significantly enhanced sensitivity when coupled with electrospray ionization-mass spectrometry (ESI-MS). Challenges that remain for the routine implementation of such miniaturized setups are related to clogging of the system and robustness in general, and thus the application of tedious sample preparation steps. To improve ruggedness, a filter placed upstream in the LC prevents particles from entering and clogging the system. This so-called online automatic filtration and filter back-flush (AFFL) system was combined with nanoLC and the direct injection principle for the sensitive confirmatory analysis of fifty different doping-relevant peptides in urine. The presented assay was fully validated for routine purposes according to selectivity and matrix interference, limit of identification (LOI), carryover, matrix effect, sample extract stability, analysis of educational external quality assessment (EQAS) samples, robustness of the online AFFL-setup and retention time stability. It was also fully compliant with the most recent minimum required performance levels (MRPL) and chromatographic/mass spectrometric identification criteria (IDCR), as imposed by the World Anti-Doping Agency (WADA). In the absence of labor-intensive sample preparation, the application of AFFL allowed for the injection of diluted urine samples without any noticeable pressure buildup in the nanoLC system. Contrary to earlier observations by our group and others, the addition of dimethylsulfoxide (DMSO) to the mobile phase did not enhance sensitivity in the presented nanoflow setup, yet was beneficial to reduce carry over. Although the robustness of the presented setup was evaluated only for the analysis of diluted urine samples, it is entirely conceivable that routine applications employing other matrices and currently running on analytical scale LC instruments could be transferred to micro/nanoLC scale systems to reach lower detection limits.

Solution Condition-Dependent Formation of Gas-Phase Protomers of Alpha-Synuclein in Electrospray Ionization

One of the main characteristics of biomolecular ions in mass spectrometry is their net charge, and a range of approaches exist to either increase or decrease this quantity in the gas phase. In the context of small molecules, it is well known that, in addition to the charge state, the charge site also has a profound effect on an ion's gas-phase behavior; however, this effect has been far less explored for peptides and intact proteins. Methods exist to determine charge sites of protein ions, and others have observed that the interplay of electrostatic repulsion and inherent basicity leads to different sites gaining or losing a charge depending on the total net charge. Here, we report two distinct protonation site isomers ("protomers") of α-synuclein occurring at the same charge state. The protomers showed important differences in their gas-phase fragmentation behavior and were furthermore distinguishable by ion mobility spectrometry. One protomer was produced under standard electrospray conditions, while the other was observed after addition of 10% dimethyl sulfoxide to the protein solution. Charge sites for both protomers were determined using ultraviolet photodissociation.

Enhancing Sensitivity of Liquid Chromatography-Mass Spectrometry of Peptides and Proteins Using Supercharging Agents

Trifluoroacetic acid (TFA) is often used as a mobile phase modifier to enhance reversed phase chromatographic performance. TFA adjusts solution pH and is an ion-pairing agent, but it is not typically suitable for electrospray ionization-mass spectrometry (ESI-MS) and liquid chromatography/MS (LC/MS) because of its significant signal suppression. Supercharging agents elevate peptide and protein charge states in ESI, increasing tandem MS (MS/MS) efficiency. Here, LC/MS protein supercharging was effected by adding agents to LC mobile phase solvents. Significantly, the ionization suppression generally observed with TFA was, for the most part, rescued by supercharging agents, with improved separation efficiency (higher number of theoretical plates) and lowered detection limits.

Detection and confirmation of α-cobratoxin in equine plasma by solid-phase extraction and liquid chromatography coupled to mass spectrometry

α-Cobratoxin (CTX) is a large peptide (71 amino acids) with strong analgesic effect and may be misused in sports such as horse racing. To prevent such misuse, a sensitive method is required for detection and confirmation of the toxin in equine samples. CTX was extracted from equine plasma using an optimized mixed-mode solid-phase extraction (SPE) procedure. Extracted CTX was reduced with dithiothreitol and alkylated with iodoacetamide, and then was digested by trypsin at 56°C for 30min. The digest was analysed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and tryptic peptides T2 (³CFITPDITSK¹²) and T4 (²⁴TWCDAFCSIR³³) were monitored for detection and confirmation of CTX. The limit of detection (LOD) was 0.05ng/mL for CTX in plasma, and the limit of confirmation (LOC) 0.2ng/mL. Unlike small peptides consisting of the 20 canonical amino acids, CTX was stable in equine plasma at ambient temperature for at least 24h. The developed analytical method was successfully applied to analysis of incurred plasma samples; CTX was detected in plasma collected 15min through 36h post subcutaneous administration of CTX (2.0mg dose) to a research horse, and confirmed 30min through 24h. Additionally, an approach named "reliable targeted SEQUEST search" has been proposed for assessing the specificity of T2 at product ion spectrum level for confirmation of CTX. T2 is uniquely specific for CTX, as evaluated with this approach and BLAST search. Furthermore, the effect of dimethyl sulfoxide (DMSO) as a mobile phase additive on electrospray (ESI) response of T2 and T4, background noise level and signal to noise ratio (S/N) was examined; DMSO increased signal intensity of T2 and T4 by a factor of less than 2. It is the first report that DMSO raised background noise level and did not improve S/N for the peptides, to the authors' knowledge. The developed analytical method may be applicable for analysis of CTX in plasma from other species such as greyhound dogs or even human beings.

DMSO Assisted Electrospray Ionization for the Detection of Small Peptide Hormones in Urine by Dilute-and-Shoot-Liquid-Chromatography-High Resolution Mass Spectrometry

The mobile phase additive (DMSO) has been described as a useful tool to enhance electrospray ionization (ESI) of peptides and proteins. So far, this technique has mainly been used in proteomic/peptide research, and its applicability in a routine clinical laboratory setting (i.e., doping control analysis) has not been described yet. This work provides a simple, easy to implement screening method for the detection of doping relevant small peptides (GHRPs, GnRHs, GHS, and vasopressin-analogues) with molecular weight less than 2 kDa applying DMSO in the mobile phase. The gain in sensitivity was sufficient to inject the urine samples after a 2-fold dilution step omitting a time consuming sample preparation. The employed analytical procedure was validated for the qualitative determination of 36 compounds, including 13 metabolites. The detection limits (LODs) ranged between 50 and 1000 pg/mL and were compliant with the 2 ng/mL minimum detection level required by the World Anti-Doping Agency (WADA) for all the target peptides. To demonstrate the feasibility of the work, urine samples obtained from patients who have been treated with desmopressin or leuprolide and urine samples that have been declared as adverse analytical findings were analyzed. Graphical Abstract ᅟ.