RATIONALE Ambient ionization mass spectrometry (AIMS) delivers realistic data from samples in their native state. In addition, AIMS methods reduce time and costs for sample preparation and have less environmental impact. However, AIMS data are often complex and require substantial processing before interpretation. METHODS We developed an interactive R script for the guided processing of mass spectrometry (MS) data. The ‘MQ_Assistant’ is based on MALDIquant, a popular R package for MS data processing. In each step, the user can try and pre-view the effect of chosen parameters before deciding on the values with the best result and proceeding to the next stage. The outcome of the MQ_Assistant is a feature matrix that can be further analyzed in R and statistics tools such as MetaboAnalyst. RESULTS Using 360 AIMS example spectra, we demonstrate the step-by-step processing for creating a feature matrix. In addition, we show how to visualize the results of tree biological replicates of a plant-microbe interaction between Arabidopsis and Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The final parameter set can be saved for reuse in MALDIquant workflows of similar data. CONCLUSIONS The MQ_Assistant helps novices and experienced users to develop workflows for (AI)MS data processing. The interactive procedure supports the quick finding of appropriate settings. These parameters can be exported and reused in future projects. The step-wise operation with visual feedback also suggests the use of the MQ_Assistant in education.

RATIONALE: The high sensitivity of the miniature mass spectrometer plays an irreplaceable role in rapid on-site detection. However, its analysis accuracy and stability should be improved due to the influence of sample pretreatment and use environment. The present study investigates the processing effects of EEMD feature enhancement methods on the determination coefficient and relative standard deviation of caffeine mass spectrometry signals. METHODS: This paper employs the EEMD method combined with polynomial curve fitting to enhance the characteristics of seven Caffeine mass spectrum signals with different concentrations and fifteen groups of Caffeine mass spectrum signals with the same concentration, and the wavelet analysis method was used for comparative verification. The determination coefficient and relative standard deviation of the two methods were compared. RESULTS: We found the EEMD method’s capability in adaptively decomposing Caffeine mass spectrum signals is better than wavelet analysis method. The determination coefficient of the EEMD enhanced feature is better than 0.999, and the relative standard deviation is better than 2%, and both are better than wavelet analysis methods. CONCLUSIONS: The feature enhancement processing using the EEMD method has significantly improved the determination coefficient and relative standard deviation of the sample curve, improving the accuracy and stability of the data and providing a new way for miniature mass spectrometer signal processing.

RATIONALE: Selective derivatization of peptide N-terminus with 4-formyl-benzenesulfonic acid (FBSA) enables chemically activated fragmentation in ESI+/- (positive and negative ion mode) under charge reduction conditions. Overlapped positive and negative tandem mass spectra pinpoint b-ions making the assignment of b-ion series fragments easy and accurate. METHODS: We developed a FBSA-peptide microwave assisted derivatization procedure. Derivatized and non-derivatized bovine serum albumin tryptic peptides and insulin non-tryptic peptide were compared after MS/MS analysis in positive and negative ion mode. High-quality dataset of sulfonated b-ions obtained in negative tandem mass spectra of singly charged FBSA-peptides were matched to detected b-ions in positive MS/MS spectra. Moreover, negative spectra signals were converted and matched against y-ions in positive tandem mass spectra to identify complete peptide sequences. RESULTS: The FBSA derivatization procedure produced a significantly improved MS/MS dataset (populated by high-intensity signals of b- and y-ions) in comparison to commonly used N-terminal sulfonation reagents. Undesired side reactions do not occur and the procedure reduces the derivatization time. It was found that b-ions comprise 15% and 13% of all fragment ions generated in positive and negative ion mode, respectively. High visibility of b-ion series in negative ion mode can be attributed to the N-terminal sulfonation which had no effect on the production of b-ion series in positive ion mode. CONCLUSIONS: The FBSA derivatization and de novo sequencing approach outlined here provides a reliable method for accurate peptide sequence assignment. Increased production of the b-ions in positive and negative ion mode greatly improves peak assignment and thus enables accurate sequence reconstruction. Implementation of the named methodology would improve the quality of de novo sequencing data and reduce the number of misinterpreted spectra.

Rational: Organisms that grow a hard carbonate shell or skeleton, such as foraminifera, corals or molluscs, incorporate trace elements into their shell during growth that absorbs the environmental change and biological activity they experienced. These geochemical signals locked within the carbonate are archives used in proxy reconstructions to study past environments and climates, to decipher taxonomy of cryptic species and to resolve evolutionary responses to climatic changes. Methods: Here we use a laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) as a time resolved acquisition to quantify the elemental composition of carbonate shells. We present the LABLASTER (Laser Ablation BLASt Through Endpoint in R) package, which imports a single time resolved LA-ICP-MS analysis, then detects when the laser has ablated through the carbonate as a function of change in signal over time, and outputs key summary statistics. We provide two worked examples within the package: a planktic foraminifera and a tropical coral. Results: We present the first R package that improves signal: noise ratios in data reduction workflows by automating the detection of when the laser has ablated through a sample using a smoothed time-series and subsequent removal of off-target data points. The functions are flexible and adjust dynamically to enhance the signal: noise ratio of the desired geochemical target. Visualisation tools for manual validation are also included. Conclusions: LABLASTER increases transparency and repeatability by algorithmically identifying when the laser has either ablated fully through a sample or across a mineral boundary and is thus no longer documenting a geochemical signal associated with the desired sample. LABLASTER’s focus on better data targeting means more accurate extraction of biological and geochemical signals.

RATIONALE: Sample preparation is one of the most crucial steps for MALDI mass spectrometry imaging (MALDI-MSI). The scientists beginning their adventure with this technique may be overwhelmed by the variety of matrices, solvents, concentrations, the ways of their applications, and the lack of widely available knowledge about the influence of these parameters on the results. Here we would like to present our experiences with detailed aspects of matrices deposition, hopefully helpful for the scientific community. METHODS: In our article, we have tested several MALDI matrices applied by the SunCollect® system: wet-interface matrix deposition in the context of lipids analysis. Among them: 2,5-dihydroxybenzoic acid (DHB), norharmane, N-(1-naphthyl) ethylenediamine dihydrochloride (NEDC), 9-aminoacridine (9AA). We have optimized the number of matrix layers and nozzle settings in terms of spectra intensity and the overall quality of obtained ion maps. RESULTS: Our research presents the influence of the number of matrix layers and nozzle settings on the results and allows for choosing the optimal parameters for the analyses. In positive ionization mode, DHB matrix could be chosen as the first selection. In the negative ionization mode, DAN matrix produces higher peak intensity in a lower mass range and seems to provide more information than 9AA. We recommended NEDC for particular tasks such as glucose analysis. Comparably to remaining matrices, norharmane significantly changes received ion maps. CONCLUSIONS: Dealing with such a great amount of data allows us to notice an interesting conclusion: the obtained ion picture for a particular ion could differ dramatically with changing the matrix, the solvent composition, or even the number of matrix layers. This must be considered when interpreting the result and forces us to compare the results obtained with different matrices with extreme caution.

Rationale: The fundamental understanding of Grignard-type organolanthanides(III) is still in its infancy. Decarboxylation of metal carboxylate ions is a powerful method to obtain organometallic ions which are well suited for gas-phase investigation by using ESI-MS in combination with DFT calculations. Methods： (RCO2)LnCl3- (R = CH3, Ln = La-Lu except Pm; Ln = La, R = CH3CH2, CH2CH, CHC, C6H5 and C6H11) ions were produced via ESI of LnCl3 and RCO2H/RCO2Na in methanol. Collision-induced dissociation (CID) was employed to examine whether RLnCl3- can be obtained via decarboxylation of (RCO2)LnCl3-. With the aid of DFT calculations, the influences of Ln and R on the formation of RLnCl3- can be uncovered. Results: When R was fixed as methyl, CID of (CH3CO2)LnCl3- (Ln = La-Lu except Pm) all gave (CH3)LnCl3- and LnCl3·- with a variation in the relative intensity ratio of (CH3)LnCl3-/LnCl3·-. The trend is following as (CH3)EuCl3-/EuCl3·- < (CH3)YbCl3-/YbCl3·- ≈ (CH3)SmCl3-/SmCl3·- < other (CH3)LnCl3-/LnCl3·-, which generally complies with the trend of Ln(III)/Ln(II) reduction potentials. When Ln was fixed as La and R groups were varied as CH3CH2, CH2CH, CHC, C6H5 and C6H11, the fragmentation behaviors of these (RCO2)LaCl3- are diverse. Except for (C6H11CO2)LaCl3-, the rest four (RCO2)LaCl3- ions all underwent decarboxylation to give RLaCl3-. The relative intensities of RLaCl3- compared to (RCO2)LaCl3- decrease as follow: CHC > CH2CH > C6H5 > CH3 > CH3CH2 >> C6H11 (not visible). Conclusion： A series of Grignard-type organolanthanide(III) ions RLnCl3- (R = CH3, Ln = La-Lu except Pm; Ln = La, R = CH3CH2, CH2CH, CHC and C6H5) were generated from (RCO2)LnCl3- via CO2 loss while (C6H5)LaCl3- not. The experimental and theoretical results suggest that the reduction potentials of Ln(III)/Ln(II) couples as well as the bulkiness and hybridization of hydrocarbyl groups play crucial roles in promoting or limiting the formation of RLnCl3- via decarboxylation.

RATIONALE Boron isotopes are a powerful tool for pH reconstruction in marine carbonates and as tracer for fluid-mineral interaction in geochemistry. Micro-analytical approaches based on laser ablation multi-collector inductively coupled plasma mass spectrometry (LA-MC-ICP-MS) often suffer from effects induced by the sample matrix. In this study, we investigated matrix-independent analyses of B isotopic ratios and applied this technique to cold-water corals. METHODS We employed a customized 193 nm femtosecond laser ablation system (Solstice, Spectra-Physics) coupled to a MC-ICP-MS (Nu Plasma II, Nu Instruments) equipped with electron multipliers for in situ measurements of B isotope ratios (11B/10B) at the micron-scale. We analyzed various reference materials of silicate and carbonate matrices using non-matrix match calibration without employing any correction mode. This approach was then applied to investigates defined increments in coral samples from a Chilean fjord. RESULTS We obtained accurate B isotope ratios with a precision of ± 0.9‰ (2 SD) for various reference materials including silicate glasses (GOR132-G, StHs6/80-G, ATHO-G, and NIST SRM 612), clay (IAEA-B-8) and carbonate (JCp-1) using the silicate glass NIST SRM 610 as calibration standard, which shows that neither laser-induced nor ICP-related matrix effects are detectable. The application to cold-water corals (Desmophyllum dianthus) reveal little intra-skeleton variations in δ11B with average values between 23.27 and 26.09‰. CONCLUSIONS Our instrumental set-up provides accurate and precise B isotopic ratios independently of the sample matrix at the micron-scale. This approach opens a wide field of application in geochemistry, including pH reconstruction in biogenic carbonates and deciphering processes related to fluid-mineral interaction.

Rationale. Femtoamp and picoamp electrospray ionization characteristics of a non-polar solvent were explored. The direct ESI-MS analysis of chloroform extract solution enabled rapid analysis of perfluorinated sulfonic acid (PFS) analytes in drinking water. Methods. Neat chloroform solvent and extracts were directly used in a typical wire-in ESI setup using micrometer emitter tips. Ionization currents were measured with femtoamp sensitivity while ramping the spray voltage from 0 to -5000 V. Methanol was used to illustrate the characteristics of spraying chloroform. The effect of spray voltage and inlet temperature was studied. A liquid-liquid extraction workflow was developed to analyze PFOS in drinking water using an ion trap mass spectrometer. Results. The ionization onset of chloroform solution was 41 ± 17 fA at 300 V. The ionization current gradually increased with voltage while remaining below 100 pA when using voltage up to -5000 V. PFOS ion signal was significantly enhanced to improve the detection limit to 25 ppt in chloroform. Coupled with a liquid-liquid extraction workflow, detection limits of 0.38-5.1 ppt, and a quantitation range of 5-400 ppt were achieved for perfluorinated sulfonic compounds in 1 mL drinking water samples. Conclusions. Femtoamp and picoamp modes expand the solvent compatibility range of electrospray ionization and can enable quantitative analysis in ppt concentrations.

Rationale: Position-Specific (PS) δ13C values of propane has proven its ability to provide valuable information on evolution history of natural gases. Two major approaches to measure PS δ13C values of propane are quantitative NMR (qNMR) and GC-Py(rolysis)-GC-IRMS. The qNMR has verified measurement accuracy, however, required large sample size and long experimental time limit its applications. The GC-Py-GC-IRMS is more versatile method with small sample size, but its accuracy has not been demonstrated. Methods: We measured PS δ13C values of propane from nine natural gases, using the both methods and evaluated the accuracy of GC-Py-GC-IRMS method. Results: The results show that large carbon isotope fractionations occurred for the both terminal and central carbons within propane during pyrolysis. The isotope fractionations during the pyrolysis are reproducible at optimum conditions, but vary between the two GC-Py-GC-IRMS systems tested, affected by experimental conditions (e.g., pyrolysis temperature, flow rate, and reactor conditions). Conclusions: Therefore, it is necessary to evaluate and calibrate each GC-Py-GC-IRMS system using propane gases whose PS δ13C values are accurately determined. This study also highlights a need of PS isotope standards for propane and other molecules.