Low-level 40Ca determinations using nitrous oxide with reaction cell inductively coupled plasma-tandem mass spectrometry.

In inductively coupled plasma mass spectrometry, the most abundant Ca isotope (40Ca) suffers from isobaric interference with argon, hindering the potential for low detection limits of Ca. A powerful approach is to remove the interference by using a reaction gas in a reaction cell. Ammonia (NH3) has proven to be an effective reaction gas by process of a charge transfer reaction. However, NH3 is highly corrosive and toxic and cannot remove isobaric 40 K. Therefore, this work proposes the use of nitrous oxide (N2O) to mass shift the target analyte 40Ca to 40Ca16O+ as a non-corrosive and non-toxic alternative. Instrument performance testing demonstrated that N2O was capable of reaching equivalent detection limits (0.015 ng g-1) and background equivalence concentrations (0.041 ng g-1) to that of NH3 and limited by the blank only. Further investigation of matrix interferences with synthetic standards highlighted that the N2O approach supports the separation of potassium (K) and magnesium (Mg)-based interferences at tested concentrations of more than 600 times and almost 800 times higher than Ca respectively, whereas NH3 was found to only support the removal of Mg. This work highlights a clear advantage of N2O for low-level Ca determinations with high matrix loads, as well as compatibility with other instrumentation sensitive to corrosion that supports reaction cell technology.

Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow.

MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.

DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results.

Routine identification of thousands of proteins in a single LC-MS experiment has long become the norm. With these vast amounts of data, more rigorous treatment of modified forms of peptides becomes possible. "Open search", a protein database search with a large precursor ion mass tolerance window, is becoming a popular method to evaluate possible sets of post-translational and chemical modifications in samples. The extraction of statistical information about the modification from peptide search results requires additional effort and data processing, such as recalibration of masses and accurate detection of precursors in MS1 signals. Here we present a software tool, DeltaMass, which performs kernel-density-based estimation of observed mass shifts and allows for the detection of poorly resolved mass deltas. The software also maps observed mass shifts to known modifications from public databases such as UniMod and augments them with additionally generated possible chemical changes to the molecule. Its interactive graphical interface provides an effective option for the visual interrogation of the data and the identification of potentially interesting mass shifts or unusual artifacts for subsequent analysis. However, the program can also be used in fully automated command-line mode to generate mass-shift peak lists as well.

Correcting mass shifts: A lock mass-free recalibration procedure for mass spectrometry imaging data.

Mass spectrometry imaging (MSI) has become widely popular because of its potential to map the spatial distribution of thousands of compounds in a single measurement directly from tissue surfaces. With every MSI experiment, it is important to maintain high mass accuracy for correct identification of the observed ions. Many times this can be compromised due to different experimental factors, leading to erroneous assignment of peaks. This makes recalibration a crucial preprocessing step. We describe a lock mass-free mass spectra recalibration method, which enables to significantly reduce these mass shift effects. The recalibration method is applied in three steps: First, we decide on an order to process all the spectra. Herein, we describe three different methods for ordering the spectra-minimum spanning tree (MST), topological greedy (TG), and crystal growth (CG). Second, we construct a reference (consensus) spectrum, from the ordered spectra, and third, all spectra are individually corrected against this consensus spectrum. The performance of the recalibration method is demonstrated on three imaging datasets acquired from matrix-assisted laser desorptionionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging of whole-body Drosophila melanogaster fly. The applied recalibration method is shown to strongly reduce the observed mass shifts in the imaging datasets. Among the three ordering methods, CG and MST perform comparatively better than TG and highly decrease the overall standard deviation of the mass error distribution. Lock mass correction of MSI data is practically difficult, as not all spectra contain the selected lock mass peak. Our method eliminates this need.

Relationship between Fusion Mass Shift and Postoperative Distal Adding-on in Lenke 1 Adolescent Idiopathic Scoliosis after Selective Thoracic Fusion.

STUDY DESIGN: This is a retrospective cohort study. PURPOSE: This study aims to investigate the risk factors for postoperative distal adding-on in Lenke 1 adolescent idiopathic scoliosis (AIS) and validate the relationship between fusion mass shift (FMS) and postoperative distal adding-on. OVERVIEW OF LITERATURE: Postoperative distal curve adding-on is one of the complications in AIS. FMS has been proposed to prevent postoperative distal adding-on, which requires further validation from different institutions. METHODS: This study included 60 patients with Lenke 1 AIS who underwent selective thoracic fusion surgery. Coronal spinal alignment parameters were analyzed preoperatively, postoperatively, and at the final follow-up. The postoperative FMS was divided into two groups: the balanced group (FMS ≤20 mm) and the unbalanced group (FMS >20 mm). An independent t-test was used to compare quantitative data between groups, and a chi-square test was used for qualitative data. Furthermore, binary logistic regression and receiver operating characteristics curve analyses were used to identify the risk factors for postoperative distal adding-on in AIS. RESULTS: At 2-year follow-up, the unbalanced group was more likely to have adding-on (17 of 24 patients) than the balanced group (six of 36 patients; p<0.001). Twenty-three patients with distal adding-on had significantly greater preoperative and postoperative lower instrumented vertebrae (LIV) rotation, FMS, and FMS angle (FMSA) than those without postoperative distal adding-on. Binary logistic regression analysis selected three independent risk factors for adding-on incidence after surgery: FMS (odds ratio [OR], 1.115; 95% confidence interval [CI], 1.049-1.185; p<0.001), FMSA (OR, 1.590; 95% CI, 1.225-2.064; p<0.001), and postoperative LIV rotation (OR, 6.581; 95% CI, 2.280-19.000; p<0.001). CONCLUSIONS: Achieving a balanced fusion mass intraoperatively is important to avoid postoperative distal adding-on, with FMS of <20 mm and FMS angle of <4.5°. Furthermore, correcting LIV rotation helps to decrease the incidence of postoperative distal addingon.

Modelling some rod set imperfections of a quadrupole mass filter.

The problem of modeling the mass peak shape of a quadrupole mass filter (QMF) with round rods is considered. A number of factors leading to the degradation of the mass peak shape are studied, namely, displacement of the electrodes with respect to their original position, changes in the diameter of the electrodes, and asymmetry of the supply potentials. Decomposition of the rod set field on multipole fields allows to obtain an analytical representation of the ion motion equations. Simulations have shown that a parallel shift of one or two electrodes leads to a shift of the peak along the mass number axis and dips at the peak apex. Unbalance of supply voltages does not significantly distort the peak shape, but it shifts the peak along the mass axis and creates a jump of the quadrupole offset potential proportional to the relative unbalance ∆ V / V of X and Y rods potentials.

A novel objective method for discriminating pathological and physiological colorectal uptake in the lower abdominal region using whole-body dynamic 18F-FDG-PET.

OBJECTIVES: To investigate whether the center-of-mass shift distance (CMSD) analysis on whole-body dynamic positron emission tomography (WBD-PET) with continuous bed motion is an objective index for discriminating pathological and physiological uptake in the lower abdominal colon. METHODS: We retrospectively analyzed the CMSD in 39 patients who underwent delayed imaging to detect incidental focal uptake that was difficult to determine as pathological and physiological on a conventional early-PET (early) image reconstructed by 5-phase WBD-PET images. The CMSD between each phase of WBD-PET images and between conventional early and delayed (two-phase) PET images were classified into pathological and physiological uptake groups based on endoscopic histology or other imaging diagnostics. The diagnostic performance of CMSD analysis on WBD-PET images was evaluated by receiver operator characteristic (ROC) analysis and compared to that of two-phase PET images. RESULTS: A total of 66 incidental focal uptake detected early image were classified into 19 and 47 pathological and physiological uptake groups, respectively. The CMSD on WBD-PET and two-phase PET images in the pathological uptake group was significantly lower than that in the physiological uptake group (p < 0.01), respectively. The sensitivity, specificity, and accuracy in CMSD analysis on WBD-PET images at the optimal cutoff of 5.2 mm estimated by the Youden index were 94.7%, 89.4%, and 89.4%, respectively, which were not significantly different (p = 0.74) from those of two-phase PET images. CONCLUSIONS: The CMSD analysis on WBD-PET was useful in discriminating pathological and physiological colorectal uptake in the lower abdominal region, and its diagnostic performance was comparable to that of two-phase PET images. We suggested that CMSD analysis on WBD-PET images would be a novel objective method to omit unnecessary additional delayed imaging.

In silico prediction and mass spectrometric characterization of botanical antimicrobial peptides.

Antimicrobial peptides (AMPs) are promising compounds for the treatment of antibiotic-resistant bacteria and are found across all organisms, including plants. Unlike most antibiotics, AMPs tend to act on more generalized and multiple targets, making development of resistance more difficult. Conventional approaches toward AMP identification include bioactivity-guided fractionation and genome mining. Complementary methods leveraging bioactivity-guided fractionation, cysteine motif-guided in silico AMP prediction, and mass spectrometric approaches can be combined to expand botanical AMP discovery. Herein, we present an integrated workflow which serves to streamline implementation toward a robust botanical AMP discovery pipeline.

Single-particle inductively coupled plasma mass spectrometry using ammonia reaction gas as a reliable and free-interference determination of metallic nanoparticles.

Intensive production of nanomaterials, especially metallic nanoparticles (MNPs), and their release into the environment pose several risks for humans and ecosystem health. Consequently, high-efficiency analytical methodologies are required for control and characterization of these emerging pollutants. Single-particle inductively coupled plasma - mass spectrometry (SP-ICP-MS) is a promising technique which allows the determination and characterization of MNPs. However, several elements or isotopes are hampered by spectral interferences, and dynamic-reaction cell (DRC) technology is becoming a useful tool for free interference determination by ICP-MS. DRC-based SP-ICP-MS methods using ammonia as a reaction gas (either on-mass approach or mass-shift approaches) have been developed for determining titanium dioxide nanoparticles (TiO2 NPs), copper oxide nanoparticles (CuO NPs), copper nanoparticles (Cu NPs), and zinc oxide nanoparticles (ZnO NPs). The effects of parameters such as ammonia flow rate and dwell time on the peak width (NP transient signal in SP-ICP-MS) were comprehensively studied. Influence of NP size and nature were also investigated.

Determination of Rare Earth Elements by Inductively Coupled Plasma-Tandem Quadrupole Mass Spectrometry With Nitrous Oxide as the Reaction Gas.

Nitrous oxide (N2O) was investigated as the reaction gas for the determination of rare earth elements (REEs) by inductively coupled plasma-tandem quadrupole mass spectrometry (ICP-QMS/QMS). The use of N2O as the reaction gas apparently improved the yields of m M16O+ for Eu and Yb in the reaction cell. As a result, the sensitivities for measurement of Eu and Yb were apparently improved in comparison to those obtained with O2 as the reaction gas. A high sensitivity measurement of the whole set of REEs was achieved, providing a typical sensitivity of 300,000 CPS mL/ng for REEs measured with an isotope having isotopic abundance close to 100%. The use of N2O as the reaction gas helped suppress Ba-related spectral interferences with the measurement of Eu, permitting the measurement of Eu in a natural sample without mathematic correction of spectral interferences. The detection limits (unit, pg/mL) for 14 REEs (except for Pm) from La to Lu were 0.028, 0.018, 0.006, 0.026, 0.006, 0.010, 0.017, 0.006, 0.016, 0.010, 0.016, 0.004, 0.023, and 0.012, respectively. The validity of the present method was confirmed by determining REEs in river water-certified reference materials, namely, SLRS-3 and SLRS-4.

Determination of the Non-metallic Elements in Herbal Tea by Inductively Coupled Plasma Tandem Mass Spectrometry.

The feasibility of using inductively coupled plasma tandem mass spectrometry (ICP-MS/MS) to overcome spectral overlaps in the determination of non-metallic elements was investigated. The contents of Si, P, S, Cl, Br, and I in herbal tea were determined by using ICP-MS/MS after microwave digestion. In the MS/MS mode, O2 and H2 were consecutively used as reaction gases. Low background equivalent concentration (BEC) and limit of detection (LOD) of analytes were obtained when using O2 mass shift, H2 mass shift, and H2 on-mass methods. The LODs for Si, P, S, Cl, Br, and I were 0.41, 0.048, 0.34, 0.76, 0.055, and 0.007 µg L-1, respectively. Standard reference materials NIST SRM 1515 (apple leaves) and NIST SRM 1547 (peach leaves) were used to evaluate the accuracy of the analytical method. The developed method was used to analyze 20 herbal teas. The ranges of values for Si, P, S, Cl, Br, and I in herbal tea were 236-4100, 1830-4360, 1290-3850, 335-4620, 0.86-8.21, and 0.091-0.65 µg g-1, respectively. The results showed that several non-metallic elements essential for the human body might be obtained by drinking herbal tea.

Determination of ultra-trace level plutonium isotopes in soil samples by triple-quadrupole inductively coupled plasma-mass spectrometry with mass-shift mode combined with UTEVA chromatographic separation.

Although triple-quadrupole inductively coupled plasma-mass spectrometry (ICP-MS/MS) has become an attractive technique for the measurement of long-lived radionuclides, the abundance sensitivity, isobaric and polyatomic ions interferences seriously restrict the application. The spectral peak tailing and uranium hydrides (UH+, UH2+) from 238U have a serious influence on the accurate measurement of 239Pu and 240Pu, especially for the ultra-trace level plutonium isotopes in the higher uranium sample. A new method was developed using ICP-MS/MS measurement in mass-shift mode with collision-reaction gas combined with a chemical separation procedure. As O2 readily converted Pu+ ion to PuO2+, while disassociated the interfering diatomic ions of interfering elements (U, Pb, Hg, Tl, etc.), the interferences from these elements were completely eliminated if plutonium was detected as PuO2+ at the m/z more than 270. By the mass filter in MS/MS mode combined with O2 as reaction gas the lower peak tailing of 238U+ (<5 × 10-12) was significantly suppressed. By this way, the 238UO2H+/238UO2+ atomic ratio was reduced to 4.82 × 10-9, which is significantly lower than that of other collision-reaction gas modes. Interferences from Pb, Hg and Tl polyatomic ions were also completely eliminated. Thus, accurate measurement of ultra-trace level 239Pu in high uranium sample solutions with the 239Pu/238U concentration ratio of 10-10 was achieved by the mass-shift mode with 0.15 mL/min O2/He + 12.0 mL/min He as collision-reaction gas, and high elimination efficiency of uranium interferences up to 1014 can be obtained by combination with the chemical separation using a single UTEVA resin column. The developed method can be applied to accurately determine the fg level 239Pu in high uranium samples, such as large-size deep seawater, deep soil and sediment, uranium debris of nuclear fuel.

Structure and m/z of Singly Charged Even-Electron Fragment Ions in Organic Mass Spectrometry: "A Rule of Mass Shift" Revisited (Secondary Publication).

Typical modes of bond cleavages of organic compounds in mass spectrometry are briefly summarized. Although these fragmentation rules can be quite useful for interpreting mass spectra of simple compounds, application to structurally complex molecules that contain multiple hetero atoms such as nitrogen or oxygen becomes increasingly difficult, because the exact location of an unpaired electron or positive or negative charges becomes obscure in precursor ions. About a decade ago, we proposed "a rule of mass shift," which correctly predicts the m/z for observed peaks corresponding to singly charged even-electron fragment ions. The basis of the rule postulates that ions observed as peaks in an ordinary mass spectrum should be sufficiently stable to survive during the flight path in a mass spectrometer. The important recognition is that each atom in a stable ion should be in an ordinary valence state, and no free valence should be allowed. Therefore, if the cleavage of a bond leads to an ion with an unstable structure, some structural changes must take place in order for the ion to be observed in the mass spectrum. Such structural changes can be the addition of hydrogen atom(s) and/or a proton for positive ions, and the addition of a hydrogen atom and/or the elimination of two hydrogen atoms in the case of negative ions. These required structural changes in each case are schematically depicted and discussed in detail. Two typical examples are shown, in which m/z's of the observed peaks are correctly predicted. The scope and limitations, as well as the significance of the rule for analyzing fragmentations in organic mass spectrometry are also discussed.

Determination of polybrominated diphenyl ethers in fish tissue using gas chromatography-isotope dilution tandem inductively coupled plasma mass spectrometry with a mass-shift mode.

Gas chromatography inductively coupled plasma triple quadrupole mass spectrometry (GC-ICP-MS/MS) operated in N2O reaction mode (mass-shift mode) was established for the analysis of six congeners of polybrominated diphenyl ethers (PBDEs): BDE 28, BDE 47, BDE 99, BDE 100, BDE 153 and BDE 154 in fish samples. The spectral interference on the determination of PBDEs was eliminated by measuring the product ion (BrO+) instead of traditional methods measuring Br+. After comparing the signal intensities of the three reaction gases (O2, H2, and N2O), the highest sensitivity was found using N2O as the reaction gas. The results showed that bromine is an element that suffers from strong spectral overlap in ICP, mainly from Ar-based polyatomic interferences. Spectral interference was assessed by measuring the bromine isotope ratio of 81Br+ and 79Br+ of the six priority PBDEs in the He collision mode and N2O reaction mode, respectively. In the conventional He collision mode, the relative isotope ratio of 79Br/81Br (the measured isotope ratio to the natural isotope ratio) of the analytes ranged from 0.955 to 0.965, which proves that using He as the collision gas cannot completely eliminate the spectral interference. In the N2O reaction mode, the relative isotope ratio of 79Br/81Br ranged from 0.991 to 1.004, demonstrating that spectral interference can be fully eliminated. Samples were processed using the modified QuEChERs method with detection limits ranging from 0.03 to 0.09 ng g-1 with a relative standard deviation of less than 3%. Six priority PBDEs in the NIST reference materials SRM 1947 (frozen fish tissue homogenate) were determined by mass-shift mode to verify this conclusion. No statistically significant difference was observed between the measured value and the certified value, with recoveries between 95% and 114%. The method was applied to the analysis of PBDEs in marine fish samples and five PBDEs were observed (BDE28,BDE-47, BDE-99, BDE-100 and BDE-153) at concentrations ranging from 0.04 to 0.54 ng g-1.

Systematic identification of suspected anthelmintic benzimidazole metabolites using LC-MS/MS.

Metabolite reference standards are often not available, which results in a lack of MS/MS spectra for library matching. Consequently, the identification of suspected metabolites proves to be challenging. The present study aims at structurally elucidating the MS/MS fragmentation behavior of selected benzimidazole anthelmintics to theoretically predict characteristic product ions for rapid and systematic tentative metabolite identification. A set of common characteristic product ions was identified from accurate mass MS/MS experiments for five parent compounds. It was hypothesized that the mass shift of any metabolic transformation at the parent molecule also is observable in the mass spectrum of the corresponding metabolite. This was tested and verified with six metabolite reference standards and subsequently, formulated as a general prediction scheme. The approach was integrated into a rapid MSe QTOF workflow and tested in mouse plasma for mebendazole and its metabolites. The presented scheme allows the prediction of characteristic product ions for suspected unknown metabolites. These can be matched with measured product ions of suspected metabolites for tentative identification. The theoretically predicted spectra can contribute to the tentative identification of unknown compounds in non-target and suspect screening approaches.

Quantification of Trace Arsenic in Whole Blood by ICP-QMS/QMS.

ICP-QMS/QMS was applied to whole blood samples to determine the quantity of trace As. It was found that Fe also causes polyatomic interference with As in conventional ICP-QMS, in addition to Ca and Cl, and ICP-QMS/QMS can remove these interferences in mass-shift mode using O2 as reaction gas. The ICP-QMS/QMS technique allows the determination of As at sub-ng mL-1 levels.

Quality control of single amino acid variations detected by tandem mass spectrometry.

Study of single amino acid variations (SAVs) of proteins, resulting from single nucleotide polymorphisms, is of great importance for understanding the relationships between genotype and phenotype. In mass spectrometry based shotgun proteomics, identification of peptides with SAVs often suffers from high error rates on the variant sites detected. These site errors are due to multiple reasons and can be confirmed by manual inspection or genomic sequencing. Here, we present a software tool, named SAVControl, for site-level quality control of variant peptide identifications. It mainly includes strict false discovery rate control of variant peptide identifications and variant site verification by unrestrictive mass shift relocalization. SAVControl was validated on three colorectal adenocarcinoma cell line datasets with genomic sequencing evidences and tested on a colorectal cancer dataset from The Cancer Genome Atlas. The results show that SAVControl can effectively remove false detections of SAVs. SIGNIFICANCE: Protein sequence variations caused by single nucleotide polymorphisms (SNPs) are single amino acid variations (SAVs). The investigation of SAVs may provide a chance for understanding the relationships between genotype and phenotype. Mass spectrometry (MS) based proteomics provides a large-scale way to detect SAVs. However, using the current analysis strategy to detect SAVs may lead to high rate of false positives. The SAVControl we present here is a computational workflow and software tool for site-level quality control of SAVs detected by MS. It accesses the confidence of detected variant sites by relocating the mass shift responsible for an SAV to search for alternative interpretations. In addition, it uses a strict false discovery rate control method for variant peptide identifications. The advantages of SAVControl were demonstrated on three colorectal adenocarcinoma cell line datasets and a colorectal cancer dataset. We believe that SAVControl will be a powerful tool for computational proteomics and proteogenomics.

Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

Simulation of the simultaneous dual-frequency resonance excitation of ions in a linear ion trap.

The process of ion resonance dipolar excitation in a linear ion trap by 2 ejection waveforms with close frequencies is studied. The physical mechanism of increasing the resolving power using the ion excitation is a nonlinearity of the electric radio frequency fields caused by space charge. Using 2 resonance forces with 2 close frequencies leads to the completion of 2 excitation processes. In the case of the perfect quadrupole electric field, the ion motion equations are linear, and as a result, the respondent ion ensemble is also a linear and valid superposition principle. Nevertheless, the resolution increases (20%) in the case of lack of a space charge in an operating mode with a dual-frequency. The numerical simulations show that the mass shift is removed, and the mass resolution is increased via dual-frequency resonance excitation when the frequency difference (approximately 2.5 kHz) is relatively small and the phase difference of 2 harmonic signals is 0-π3 even at a high linear ion density of up to 50 000 ions per radius field r0 .

Mass-Tag Labeling Using Acyl-PEG Exchange for the Determination of Endogenous Protein S-Fatty Acylation.

The covalent coupling of fatty acids to proteins provides an important mechanism of regulation in cells. In eukaryotes, cysteine fatty acylation (S-fatty acylation) has been shown to be critical for protein function in a variety of cellular pathways as well as microbial pathogenesis. While methods developed over the past decade have improved the detection and profiling of S-fatty acylation, these are hampered in their ability to characterize endogenous protein S-fatty acylation levels under physiological conditions. Furthermore, understanding the contribution of specific sites and levels of S-fatty acylation remains a major challenge. To evaluate S-fatty acylation of endogenous proteins as well as to determine the number of S-fatty acylation events, we developed the acyl-PEG exchange (APE) that utilizes cysteine-specific chemistry to exchange S-fatty acylation sites with mass-tags of defined size, which can be readily observed by western blotting. APE provides a readily accessible approach to investigate endogenous S-fatty acylation from any sample source, with high sensitivity and broad applicability that complements the current toolbox of methods for thioester-based post-translational modifications. © 2017 by John Wiley & Sons, Inc.