Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility

Identification of K-Ras and B-Raf mutations in colorectal cancer (CRC) is essential to predict patients' response to anti-EGFR therapy and formulate appropriate therapeutic strategies to improve prognosis and survival. Here, we combined parallel reaction monitoring (PRM) with high-field asymmetric waveform ion mobility (FAIMS) to enhance mass spectrometry sensitivity and improve the identification of low-abundance K-Ras and B-Raf mutations in biological samples without immunoaffinity enrichment. In targeted LC-MS/MS analyses, FAIMS reduced the occurrence of interfering ions and enhanced precursor ion purity, resulting in a 3-fold improvement in the detection limit for K-Ras and B-Raf mutated peptides. In addition, the ion mobility separation of isomeric peptides using FAIMS facilitated the unambiguous identification of K-Ras G12D and G13D peptides. The application of targeted LC-MS/MS analyses using FAIMS is demonstrated for the detection and quantitation of B-Raf V600E, K-Ras G12D, G13D, and G12V in CRC cell lines and primary specimens.

The Effect of Surgeon Volume on Revision for Periprosthetic Joint Infection: An Analysis of 602,919 Primary Total Knee Arthroplasties

BACKGROUND

Periprosthetic joint infection (PJI) is a devastating complication of total knee arthroplasty (TKA). An association between low surgeon volume and higher rates of infection following primary TKA has been suggested. The purpose of the present study was to determine if there was a relationship between surgeon volume and the rate of revision for infection after primary TKA.

METHODS

We searched the Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) to identify all primary TKA procedures that were performed for the treatment of osteoarthritis from September 1, 1999, to December 31, 2020, and were subsequently revised because of infection. Surgeon volume was defined as the annual volume of procedures performed by a surgeon during the same year in which the primary TKA (which was subsequently revised for infection) was performed. Surgeon volume was defined as <25, 25 to 49, 50 to 74, 75 to 99, or ≥100 primary TKA procedures/year. The cumulative percent revision (CPR) for infection was determined with use of Kaplan-Meier estimates. Cox proportional hazards methods were used to compare rates of revision for infection by surgeon volume, with subanalyses for patellar resurfacing and polyethylene use. Further analyses for patients <65 years of age and male patients were undertaken.

RESULTS

Overall, 602,919 primary TKA procedures were performed for the treatment of osteoarthritis, of which 5,295 were revised because of infection. High-volume surgeons (≥100 TKAs/year) had a significantly lower rate of revision for infection, with a CPR at 1 and 19 years of 0.4% (95% confidence interval [CI], 0.3 to 0.4) and 1.5% (95% CI, 1.2 to 2.0), respectively, compared with 0.6% (95% CI, 0.5 to 0.7) and 2.1% (95% CI, 1.8 to 2.3), respectively, for low-volume surgeons (<25 TKAs/year). Hazard ratios (HRs), adjusted for age and sex, comparing these 2 groups varied, depending on the time point, between 3.07 (95% CI, 2.02 to 4.68) and 1.44 (95% CI, 1.26 to 1.63) but remained significant (p < 0.001). When the analysis was adjusted for age, sex, American Society of Anesthesiologists (ASA) classification, and body mass index (BMI), there remained an increased risk of revision for PJI for all lower surgeon volume levels in comparison with the high- surgeon-volume group (≥100 TKAs/year). The results were similar when stratified by patellar resurfacing and cross-linked polyethylene (XLPE) and adjusted for age and sex.

CONCLUSIONS

High-volume surgeons had lower rates of revision for infection. A better understanding of how surgical volume contributes to decreasing this complication is important and requires in-depth study.

LEVEL OF EVIDENCE

Prognostic Level III . See Instructions for Authors for a complete description of levels of evidence.

Proteogenomics and Differential Ion Mobility Enable the Exploration of the Mutational Landscape in Colon Cancer Cells

The sensitivity and depth of proteomic analyses are limited by isobaric ions and interferences that preclude the identification of low abundance peptides. Extensive sample fractionation is often required to extend proteome coverage when sample amount is not a limitation. Ion mobility devices provide a viable alternate approach to resolve confounding ions and improve peak capacity and mass spectrometry (MS) sensitivity. Here, we report the integration of differential ion mobility with segmented ion fractionation (SIFT) to enhance the comprehensiveness of proteomic analyses. The combination of differential ion mobility and SIFT, where narrow windows of ∼m/z 100 are acquired in turn, is found particularly advantageous in the analysis of protein digests and typically provided more than 60% gain in identification compared to conventional single-shot LC-MS/MS. The application of this approach is further demonstrated for the analysis of tryptic digests from different colorectal cancer cell lines where the enhanced sensitivity enabled the identification of single amino acid variants that were correlated with the corresponding transcriptomic data sets.

Integration of Segmented Ion Fractionation and Differential Ion Mobility on a Q-Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer

High-field asymmetric waveform ion mobility spectrometry (FAIMS) has gained popularity in the proteomics field for its capability to improve mass spectrometry sensitivity and to decrease peptide co-fragmentation. The recent implementation of FAIMS on Tribrid Orbitrap instruments enhanced proteome coverage and increased the precision of quantitative measurements. However, the FAIMS interface has not been available on older generation Orbitrap mass spectrometers such as the Q-Exactive. Here, we report the integration of the FAIMS Pro device with embedded electrical and gas connections to a Q-Exactive HF mass spectrometer. Proteomic experiments performed on HeLa tryptic digests with the modified mass spectrometer improved signal to noise and reduced interfering ions, resulting in an increase of 42% in peptide identification. FAIMS was also combined with segmented ion fractionation where 100 m/z windows were obtained in turn to further increase the depth of proteome analysis by reducing the proportion of chimeric MS/MS spectra from 50 to 27%. We also demonstrate the application of FAIMS to improve quantitative measurements when using isobaric peptide labeling. FAIMS experiments performed on a two-proteome model revealed that FAIMS Pro provided a 65% improvement in quantification accuracy compared to conventional LC-MS/MS experiments.

A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements

The depth of proteomic analyses is often limited by the overwhelming proportion of confounding background ions that compromise the identification and quantification of low abundance peptides. To alleviate these limitations, we present a new high field asymmetric waveform ion mobility spectrometry (FAIMS) interface that can be coupled to the Orbitrap Tribrid mass spectrometers. The interface provides several advantages over previous generations of FAIMS devices, including ease of operation, robustness, and high ion transmission. Replicate LC-FAIMS-MS/MS analyses (n = 100) of HEK293 protein digests showed stable ion current over extended time periods with uniform peptide identification on more than 10,000 distinct peptides. For complex tryptic digest analyses, the coupling of FAIMS to LC-MS/MS enabled a 30% gain in unique peptide identification compared with non-FAIMS experiments. Improvement in sensitivity facilitated the identification of low abundance peptides, and extended the limit of detection by almost an order of magnitude. The reduction in chimeric MS/MS spectra using FAIMS also improved the precision and the number of quantifiable peptides when using isobaric labeling with tandem mass tag (TMT) 10-plex reagent. We compared quantitative proteomic measurements for LC-MS/MS analyses performed using synchronous precursor selection (SPS) and LC-FAIMS-MS/MS to profile the temporal changes in protein abundance of HEK293 cells following heat shock for periods up to 9 h. FAIMS provided 2.5-fold increase in the number of quantifiable peptides compared with non-FAIMS experiments (30,848 peptides from 2,646 proteins for FAIMS versus 12,400 peptides from 1,229 proteins with SPS). Altogether, the enhancement in ion transmission and duty cycle of the new FAIMS interface extended the depth and comprehensiveness of proteomic analyses and improved the precision of quantitative measurements.

Optimization of a New Aerodynamic Cylindrical FAIMS Device for Small Molecule Analysis

The implementation of an aerodynamic mechanism to improve ion sampling between nanoelectrospray (n-ESI) and FAIMS was recently reported for proteomic analyses. This investigation explores the new FAIMS interface for small molecule analysis at high liquid flow rates and includes an examination of key differences in ionization between heated-ESI (HESI) and n-ESI. The sheath gas, critical for desolvation with HESI, affects FAIMS operation as higher FAIMS gas flow rates are required to achieve sufficient desolvation. Gas flow rate experiments also uncovered m/z discrimination with the conventional design as larger (slower moving) m/z ions experienced larger signal intensity losses than smaller m/z ions due to the desolvation gas flow having a greater drag effect on slower moving ions. The modified inlet in new FAIMS dampens the gas drag, making the HESI source more amenable as less m/z bias and significantly lower %RSD values were observed. Furthermore, a larger radius inner electrode in new FAIMS enables significantly higher E/N (electric field/number gas density) to be achieved using the existing waveform generator. Thus, new FAIMS signal intensities using only nitrogen improved 1.25- to 2-fold compared with the conventional design and 50% helium. Adding helium to the new FAIMS gave no significant improvements. The larger inner electrode also decreased ion focusing capabilities, and the effect on peak separation and ion intensity was examined in detail. The peak capacity of new FAIMS was approximately double that of conventional FAIMS; separation of seven low m/z ions gave a peak capacity of 37.7 using the gas additive 2-propanol. Graphical Abstract ᅟ.

Separation of opiate isomers using electrospray ionization and paper spray coupled to high-field asymmetric waveform ion mobility spectrometry

One limitation in the growing field of ambient or direct analysis methods is reduced selectivity caused by the elimination of chromatographic separations prior to mass spectrometric analysis. We explored the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS), an ambient pressure ion mobility technique, to separate the closely related opiate isomers of morphine, hydromorphone, and norcodeine. These isomers cannot be distinguished by tandem mass spectrometry. Separation prior to MS analysis is, therefore, required to distinguish these compounds, which are important in clinical chemistry and toxicology. FAIMS was coupled to a triple quadrupole mass spectrometer, and ionization was performed using either a pneumatically assisted heated electrospray ionization source (H-ESI) or paper spray, a direct analysis method that has been applied to the direct analysis of dried blood spots and other complex samples. We found that FAIMS was capable of separating the three opiate structural isomers using both H-ESI and paper spray as the ionization source.

Using gas modifiers to significantly improve sensitivity and selectivity in a cylindrical FAIMS device

Recent reports describing enhanced performance when using gas additives in a DMS device (planar electrodes) have indicated that comparable benefits are not attainable using FAIMS (cylindrical electrodes), owing to the non-homogeneous electric fields within the analyzer region. In this study, a FAIMS system (having cylindrical electrodes) was modified to allow for controlled delivery of gas additives. An experiment was carried out that illustrates the important distinction between gas modifiers present as unregulated contaminants and modifiers added in a controlled manner. The effect of contamination was simulated by adjusting the ESI needle position to promote incomplete desolvation, thereby permitting ESI solvent vapor into the FAIMS analyzer region, causing signal instability and irreproducible CV values. However, by actively controlling the delivery of the gas modifier, reproducible CV spectra were obtained. The effects of adding different gas modifiers were examined using 15 positive ions having mass-to-charge (m/z) values between 90 and 734. Significant improvements in peak capacity and increases in ion transmission were readily attained by adding acetonitrile vapor, even at trace levels (≤0.1%). Increases in signal intensity were greatest for the low m/z ions; for the six lowest molecular weight species, signal intensities increased by ∼10- to over 100-fold compared with using nitrogen without gas additives, resulting in equivalent or better signal intensities compared with ESI without FAIMS. These results confirm that analytical benefits derived from the addition of gas modifiers reported with a uniform electric field (DMS) also are observed using a non-homogenous electric field (FAIMS) in the analyser region.

Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes

Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides.

Characterization of a temperature-controlled FAIMS system

High-field asymmetric waveform ion mobility spectrometry (FAIMS) focuses and separates gas-phase analyte ions from chemical background, offering substantial improvements in the detection of targeted species in biological matrices. Ion separations have been typically performed at atmospheric pressure and ambient temperature, although routine small molecule quantitation by LC-MS (and thus LC-FAIMS-MS) is generally performed at liquid flow rates (e.g., in excess of 200 microL/min) in which atmospheric pressure ionization sources (e.g., APCI and ESI) need to be run at elevated temperatures to enhance ion desolvation. Heat from the ionization source and/or the mass spectrometer capillary interface is shown to have a significant impact on the performance of a conventional FAIMS electrode set. This study introduces a new FAIMS system that uses gas heating/cooling to quickly reach temperature equilibrium independent of the external temperature conditions. A series of equations and balance plots, which look at the effect of temperature and other variables, on the normalized field strength (E/N), are introduced and used to explain experimental observations. Examples where the ion behavior deviates from the predicted behavior are presented and explanations based on clusters or changes in ion-neutral interactions are given. Consequences of the use of temperature control, and in particular advantages of using different temperature settings on the inner and outer electrodes, for the purpose of manipulating ion separation are described.