An official website of the United States government
Protein tandem mass spectrometry (MS/MS) often generates sequence-informative fragments from backbone bond cleavages near the termini. This lack of fragmentation in the protein interior is particularly apparent in native top-down MS. Improved sequence coverage, critical for reliable annotation of posttranslational modifications (PTMs) and sequence variants, may be obtained from internal fragments generated by multiple backbone cleavage events. However, internal fragment assignments can be error prone due to isomeric/isobaric fragments from different parts of a protein sequence. Also, internal fragment generation propensity depends on the chosen MS/MS activation strategy. Here, we examine internal fragment formation in electron capture dissociation (ECD) and electron transfer dissociation (ETD) following native and denaturing MS, as well as liquid chromatography (LC)/MS of several proteins. Experiments were undertaken on multiple instruments, including Q-ToF, Orbitrap, and high-field FT-ICR across four laboratories. ECD was performed at both ultrahigh vacuum and at similar pressure to ETD conditions. Two complementary software packages were used for data analysis. When feasible, ETD-higher-energy collision dissociation (ETD-HCD) MS3 was performed to validate/refute potential internal fragment assignments, including differentiating MS3 fragmentation behavior of radical vs. even-electron primary fragments. We show that, under typical operating conditions, internal fragments cannot be confidently assigned in ECD, nor ETD. On the other hand, such fragments, along with some b-type terminal fragments (not typically observed in ECD/ETD spectra) appear at atypical ECD operating conditions, suggesting they originate from a separate ion-electron activation process. Furthermore, atypical fragment ion types, e.g., x ions, are observed at such conditions as well as upon EThcD, presumably due to vibrational activation of radical z-type ions.
more »
« less
An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer?
Abstract High‐resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive‐ion and negative‐ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified ~1000 common ions in both negative‐ and positive‐ion modes over a wide range ofm/zvalues and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance‐weighted average indices (H/C, O/C, aromaticity, andm/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments.
more »
« less
- PAR ID:
- 10458015
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Limnology and Oceanography: Methods
- Volume:
- 18
- Issue:
- 6
- ISSN:
- 1541-5856
- Page Range / eLocation ID:
- p. 235-258
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Lipid screening of biological substrates is an important step during biomarker detection and identification. In this work, a fast workflow is described capable of rapid screening for lipid components from biological tissues at ambient pressure based on liquid microjunction extraction in tandem with nano-electrospray ionization (nESI) with ultra-high resolution mass spectrometry, i.e. , liquid extraction surface analysis (LESA) coupled to Fourier-transform ion cyclotron resonance (tandem) mass spectrometry (LESA-FT-ICR-MS/MS). Lipid profiles are presented for thin tissue sections of mouse brain (MB) and liver (ML) samples, analyzed in both positive and negative mode by data-dependent acquisition (DDA) tandem FT-ICR-MS/MS. Candidate assignments were based on fragmentation patterns using mostly SimLipid software and accurate mass using mostly the LipidMaps database (average sub-ppm mass error). A typical, single point surface analysis (<1 mm spatial sampling resolution) lasted less than 15 minutes and resulted in the assignment of (unique and mulitple) lipid identifications of ∼190 (MB) and ∼590 (ML) m / z values. Despite the biological complexity, this led to unique identifications of distinct lipid molecules (sub-ppm mass error) from 38 different lipid classes, corresponding to 10–30% of the lipid m / z identifications.more » « less
-
null (Ed.)Guaiacyl acetone (GA) is a phenolic carbonyl emitted in significant quantities by wood combustion that undergoes rapid aqueous-phase oxidation to produce aqueous secondary organic aerosol (aqSOA). We investigate the photosensitized oxidation of GA by an organic triplet excited state (3C*) and the formation and aging of the resulting aqSOA in wood smoke-influenced fog/cloud water. The chemical transformations of the aqSOA were characterized in situ using a high-resolution time-of-flight aerosol mass spectrometer. Additionally, aqSOA samples collected over different time periods were analyzed using high-performance liquid chromatography coupled with a photodiode array detector and a high-resolution Orbitrap mass spectrometer (HPLC-PDA-HRMS) to provide details on the molecular composition and optical properties of brown carbon (BrC) chromophores. Our results show efficient formation of aqSOA from GA, with an average mass yield around 80%. The composition and BrC properties of the aqSOA changed significantly over the course of reaction. Three generations of aqSOA products were identified via Positive Matrix Factorization analysis of the AMS data. Oligomerization and functionalization dominated the production of the first-generation aqSOA, whereas fragmentation and ring-opening reactions controlled the formation of more oxidized second- and third-generation products. Significant formation of BrC was observed in the early stages of the photoreaction, while organic acids were produced throughout the experiment. High-molecular-weight molecules (m/z > 180) with high aromaticity were identified via HPLC-PDA-HRMS and were found to account for a majority of the UV-vis absorption of the aqSOA.more » « less
-
Several areas around the world rely on seawater desalination to meet drinking water needs, but a detailed analysis of dissolved organic matter (DOM) changes and disinfection by-product (DBP) formation due to chlorination during the desalination processes has yet to be evaluated. To that end, DOM composition was analyzed in samples collected from a desalination plant using bulk measurements ( e.g. dissolved organic carbon, total dissolved nitrogen, total organic bromine), absorbance and fluorescence spectroscopy, and ultrahigh resolution mass spectrometry (HRMS). Water samples collected after chlorination ( e.g. post pretreatment (PT), reverse osmosis (RO) reject (brine wastewater) (BW), RO permeate (ROP), and drinking water (DW)), revealed that chlorination resulted in decreases in absorbance and increases in fluorescence apparent quantum yield spectra. All parameters measured were low or below detection in ROP and in DW. However, total solid phase extractable (Bond Elut Priority PolLutant (PPL) cartridges) organic bromine concentrations increased significantly in PT and BW samples and HRMS analysis revealed 392 molecular ions containing carbon, hydrogen, oxygen, bromine (CHOBr) and 107 molecular ions containing CHOBr + sulfur (CHOSBr) in BW PPL extracts. A network analysis between supposed DBP precursors suggested that the formation of CHOBr formulas could be explained largely by electrophilic substitution reactions, but also HOBr addition reactions. The reactions of sulfur containing compounds are more complex, and CHOSBr could possibly be due to the bromination of surfactant degradation products like sulfophenyl carboxylic acids (SPC) or even hydroxylated SPCs. Despite the identification of hundreds of DBPs, BW did not show any acute or chronic toxicity to mysid shrimp. High resolution MS/MS analysis was used to propose structures for highly abundant bromine-containing molecular formulas but given the complexity of DOM and DBPs found in this study, future work analyzing desalination samples during different times of year ( e.g. during algal blooms) and during different treatments is warranted.more » « less
-
Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD.more » « less
