Top-Down Proteomic Characterization of Truncated Proteoforms

Chen, Dapeng; Geis-Asteggiante, Lucía; Gomes, Fábio Pereira; Ostrand‐Rosenberg, Suzanne; Fenselau, Catherine

doi:10.1021/acs.jproteome.9b00487

Cited by 16 publications

(19 citation statements)

References 54 publications

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“…In this study, proteoforms were considered identified when the difference between observed and theoretical masses was ≤10 ppm and P-Score was ≤1 × 10 –04 . , While an “absolute mass search” on ProsightPD limits the search space to species matching the precursor mass, a “biomarker search” expands the search space to fragments of protein sequences that match the precursor mass. In this study, the majority of the proteoforms (>70%) were identified by the biomarker search, which indicates the presence of several truncated proteoforms . In addition to strong evidence of protein identification, concordance between theoretical and observed masses of precursor ions is a significant advance to a successful proteoform identification.…”

Section: Resultsmentioning

confidence: 56%

“…In this study, the majority of the proteoforms (>70%) were identified by the biomarker search, which indicates the presence of several truncated proteoforms. 32 In addition to strong evidence of protein identification, concordance between theoretical and observed masses of precursor ions is a significant advance to a successful proteoform identification. For instance, the mass difference between arginine and citrulline is +0.984 Da and between lysine and allysine is −1.0316 Da.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

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EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

et al. 2020

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Seminal plasma is a critical and complex fluid that carries sperm to eggs to initiate the fertilization process. Here, we present a top-down mass spectrometry (TDMS) strategy for identifying proteins and posttranslational modifications (PTMs) in bovine seminal plasma. In this study, proteins were separated using sheathless capillary zone electrophoresis (CZE)-MS and reversed-phase liquid chromatography (LC)-MS, and then fragmented using electron-transfer/higher-energy collisional dissociation (EThcD) and 213 nm ultraviolet photodissociation (213 nm UVPD) to provide more comprehensive information about the proteomic landscape of this biological fluid. Four hundred and seventeen proteoforms were identified by sheathless CZE-MS, and one hundred and seventy-two species were unique to this method. LC-MS identified 3090 proteoforms, including 1707 unique species. All identifications were within ±10 ppm (mass error) and with a P-Score ≤1 × 10–04. Pooling results (triplicate measurements) from sheathless CZE-MS and LC-MS resulted in the identification of 1433 proteoforms (EThcD) and 2151 proteoforms (213 nm UVPD) with 612 species unique for EThcD and 1021 for 213 nm UVPD. The average sequence coverage was found to be higher for EThcD (28%) than for 213 nm UVPD (23%). The use of sheathless CZE-MS and LC-MS with EThcD and 213 nm UVPD provided complementary protein profiling and proteoform data that were more comprehensive than those of either method alone.

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Section: Resultsmentioning

confidence: 56%

Section: ■ Results and Discussionmentioning

confidence: 99%

EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

et al. 2020

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“…Another advantage of using SPE-based extraction is that proteins contained in the aerosol particles can be preserved. Mass spectrometry-based rapid identification of proteins without enrichment and enzymatic digestion were developed 37 . As a result, signature proteins characterized by TB patients could be combined with lipid biomarkers to provide a more reliable diagnostic approach for the identification of active TB patients.…”

Section: Discussionmentioning

confidence: 99%

Detection of Tuberculosis by The Analysis of Exhaled Breath Particles with High-resolution Mass Spectrometry

Chen

Bryden

Wood

2020

Preprint

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Tuberculosis remains a global health threat killing over 1 million people per year. Current sputum-based diagnostics are specific but lack sensitivity resulting in treatment of many sputum negative cases. In this proof-of-concept study, we used high-resolution mass spectrometry to identify specific lipids in peripheral lung fluid samples of TB patients and controls, captured using a novel non-invasive sampling system. Exhaled respiratory particles were collected in liquid and after concentration and lipid extraction directly infused into a high-resolution mass spectrometer. High-resolution mass spectrometric data collection was conducted in a dual ion mode and chemical compositions were constructed using accurate mass measurement. Over 400 features with high segregating capacity were extracted and optimized using feature selection algorithm and machine learning, from which the accuracy of detection of positive tuberculosis patients was estimated. This current strategy provides sensitivity offered by high-resolution mass spectrometry and can be readily susceptible for developing a novel clinical assay exploring peripheral lung fluid for the detection of active TB cases

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“…Monoisotopic masses were deconvoluted using Xcalibur software 3.0 (Thermo Fisher Scientific) and the fragmentation ions were interpreted using ProSight Lite (northwestern.edu). 20,21 For richer details on top-down mass spectrometric data analysis, the reader may refer to our previous studies and the supplemental information. Figure 1.…”

Section: Methodsmentioning

confidence: 99%

Capture of Viruses and Microorganisms in Aerosols Using A Newly Designed Collection System: A Proof-of-concept Study

Chen

et al. 2021

Preprint

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Aerosols contain human pathogens that cause public health disasters such as tuberculosis (TB) and the ongoing COVID-19 pandemic. The current technologies for the collection of viruses and microorganisms in aerosols face critical limitations, necessitating the development of a new type of sampling system to advance the capture technology. Herein, we presented a new type of collection system, which exploits the affinity between carbon chains and organic molecules on the surfaces of viruses and microorganisms. We demonstrated that the physical capture efficiency of the collection system was over 99% for particle sizes from 0.3 to 10 um. We further evaluated the biochemical capture efficiency of the collection system using mass spectrometry approaches and showed that the biochemical information of viruses and microorganisms was well preserved. Coupled with well-established molecular technologies, this new type of capture technology can be used for the investigation of aerosol-related disease transmission models, as well as the development of innovative screening and monitoring tools for human diseases and public health issues.

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Top-Down Proteomic Characterization of Truncated Proteoforms

Cited by 16 publications

References 54 publications

EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

EThcD and 213 nm UVPD for Top-Down Analysis of Bovine Seminal Plasma Proteoforms on Electrophoretic and Chromatographic Time Frames

Detection of Tuberculosis by The Analysis of Exhaled Breath Particles with High-resolution Mass Spectrometry

Capture of Viruses and Microorganisms in Aerosols Using A Newly Designed Collection System: A Proof-of-concept Study

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