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Smith BL, Hankinson T, Maher S. Portable Instrumentation for Ambient Ionization and Miniature Mass Spectrometers. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:69-102. [PMID: 38640067 DOI: 10.1146/annurev-anchem-061522-040824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
We critically evaluate the current status of portable mass spectrometry (pMS), particularly where this aligns with ambient ionization. Assessing the field of pMS can be quite subjective, especially in relation to the portable aspects of design, deployment, and operation. In this review, we discuss what it means to be portable and introduce a set of criteria by which pMS and ambient ionization sources can be assessed. Moreover, we consider the recent literature in terms of the most popular and significant advances in portable instrumentation for ambient ionization and miniature mass spectrometers. Finally, emerging trends and exciting future prospects are discussed and some recommendations are offered.
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Affiliation(s)
- Barry L Smith
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, United Kingdom;
| | - Thomas Hankinson
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, United Kingdom;
| | - Simon Maher
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, United Kingdom;
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Remoroza CA, Burke MC, Mak TD, Sheetlin SL, Mirokhin YA, Cooper BT, Goecker ZC, Lowenthal MS, Yang X, Wang G, Tchekhovskoi DV, Stein SE. Comparison of N-Glycopeptide to Released N-Glycan Abundances and the Influence of Glycopeptide Mass and Charge States on N-Linked Glycosylation of IgG Antibodies. J Proteome Res 2024; 23:1443-1457. [PMID: 38450643 PMCID: PMC10997438 DOI: 10.1021/acs.jproteome.3c00904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
We report the comparison of mass-spectral-based abundances of tryptic glycopeptides to fluorescence abundances of released labeled glycans and the effects of mass and charge state and in-source fragmentation on glycopeptide abundances. The primary glycoforms derived from Rituximab, NISTmAb, Evolocumab, and Infliximab were high-mannose and biantennary complex galactosylated and fucosylated N-glycans. Except for Evolocumab, in-source ions derived from the loss of HexNAc or HexNAc-Hex sugars are prominent for other therapeutic IgGs. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances over a dynamic range of 500. Different charge states of human IgG-derived glycopeptides containing a wider variety of abundant attached glycans were also investigated to examine the effects of the charge state on ion abundances. These revealed a linear dependence of glycopeptide abundance on the mass of the glycan with higher charge states favoring higher-mass glycans. Findings indicate that the mass spectrometry-based bottom-up approach can provide results as accurate as those of glycan release studies while revealing the origin of each attached glycan. These site-specific relative abundances are conveniently displayed and compared using previously described glycopeptide abundance distribution spectra "GADS" representations. Mass spectrometry data are available from the MAssIVE repository (MSV000093562).
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Affiliation(s)
| | | | | | | | | | - Brian T. Cooper
- Mass Spectrometry Data Center
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | | | - Mark S. Lowenthal
- Bioanalytical Science Group, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive Gaithersburg, MD 20899, US
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Xue J, Zhu J, Hu L, Yang J, Lv Y, Zhao F, Liu Y, Zhang T, Cai Y, Fang M. EISA-EXPOSOME: One Highly Sensitive and Autonomous Exposomic Platform with Enhanced in-Source Fragmentation/Annotation. Anal Chem 2023; 95:17228-17237. [PMID: 37967119 DOI: 10.1021/acs.analchem.3c02697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Lacking a highly sensitive exposome screening technique is one of the biggest challenges in moving exposomic research forward. Enhanced in-source fragmentation/annotation (EISA) has been developed to facilitate molecular identification in untargeted metabolomics and proteomics. In this work, with a mixture of 50 pesticides at three concentration levels (20, 4, and 0.8 ppb), we investigated the analytical performance of the EISA technique over the well-accepted targeted MS/MS mode (TMM) in the detection and identification of chemicals at low levels using a quadrupole time-of-flight (qTOF) instrument. Compared with the TMM method, the EISA technique can recognize additional 1, 20, and 23 chemicals, respectively, at the three concentration levels (20, 4, and 0.8 ppb, respectively) investigated. At the 0.8 ppb level, intensities of precursor ions and fragments observed using the EISA technique are 30-1,154 and 3-80 times higher, respectively, than those observed at the TMM mode. A higher matched fragment ratio (MFR) between the EISA technique and the TMM method was recognized for most chemicals. We further developed a chemical annotation informatics algorithm, EISA-EXPOSOME, which can automatically search each precursor ion (m/z) in the MS/MS library against the EISA MS1 spectra. This algorithm then calculated a weighted score to rank the candidate features by comparing the experimental fragment spectra to those in the library. The peak intensity, zigzag index, and retention time prediction model as well as the peak correlation coefficient were further adopted in the algorithm to filter false positives. The performance of EISA-EXPOSOME was demonstrated using a pooled dust extract with a pesticide mixture (n = 200) spiked at 5 ppb. One urine sample spiked with a contaminant mixture (n = 50) at the 5 ppb level was also used for the validation of the pipeline. Proof-of-principal application of EISA-EXPOSOME in the real sample was further evaluated on the pooled dust sample with a modified T3DB database (n = 1650). Our results show that the EISA-EXPOSOME algorithm can remarkably improve the detection and annotation coverage at trace levels beyond the traditional approach as well as facilitate the high throughput screening of suspected chemicals.
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Affiliation(s)
- Jingchuan Xue
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Jiamin Zhu
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Lixin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Junjie Yang
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore
| | - Yunbo Lv
- Nanyang Environment And Water Research Institute, Nanyang Technological University, 637141 Singapore
| | - Fanrong Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Yuxian Liu
- Key Laboratory of Ministry of Education for Water Quality Security and Protection in Pearl River Delta, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Tao Zhang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yanpeng Cai
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Mingliang Fang
- Department of Environmental Science and Engineering, Fudan University, 220 Handan Rd., Shanghai 200433, China
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Brodie NI, Sarpe V, Crowder DA, Schriemer D. All-in-One Pseudo-MS 3 Method for the Analysis of Gas-Phase Cleavable Protein Crosslinking Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2146-2155. [PMID: 37590165 PMCID: PMC11250984 DOI: 10.1021/jasms.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Crosslinking mass spectrometry (XL-MS) supports structure analysis of individual proteins and highly complex whole-cell interactomes. The identification of crosslinked peptides from enzymatic digests remains challenging, especially at the cell level. Empirical methods that use gas-phase cleavable crosslinkers can simplify the identification process by enabling an MS3-based strategy that turns crosslink identification into a simpler problem of detecting two separable peptides. However, the method is limited to select instrument platforms and is challenged by duty cycle constraints. Here, we revisit a pseudo-MS3 concept that incorporates in-source fragmentation, where a fast switch between gentle high-transmission source conditions and harsher in-source fragmentation settings liberates peptides for standard MS2-based peptide identification. We present an all-in-one method where retention time matches between the crosslink precursor and the liberated peptides establish linkage, and MS2 sequencing identifies the source-liberated peptides. We demonstrate that DC4, a very labile cleavable crosslinker, generates high-intensity peptides in-source. Crosslinks can be identified from these liberated peptides, as they are chromatographically well-resolved from monolinks. Using bovine serum albumin (BSA) as a crosslinking test case, we detect 27% more crosslinks with pseudo-MS3 over a best-in-class MS3 method. While performance is slightly lower for whole-cell lysates (generating two-thirds of the identifications of a standard method), we find that 60% of these hits are unique, highlighting the complementarity of the method.
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Affiliation(s)
- Nicholas I Brodie
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N-4N1
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Xie J, Guo Y, Ma Y, Jiang H, Zhang L, Mao L, Zhu L, Zheng Y, Liu X. Spontaneous In-Source Fragmentation Reaction Mechanism and Highly Sensitive Analysis of Dicofol by Electrospray Ionization Mass Spectrometry. Molecules 2023; 28:molecules28093765. [PMID: 37175171 PMCID: PMC10180504 DOI: 10.3390/molecules28093765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Although dicofol has been widely banned all over the world as a kind of organochlorine contaminant, it still exists in the environment. This study developed a high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS/MS) detection technique for dicofol, an environmental pollutant, for the first time using in-source fragmentation. The results confirmed that m/z 251 was the only precursor ion of dicofol after in-source fragmentation, and m/z 139 and m/z 111 were reasonable product ions. The main factors triggering the in-source fragmentation were the H+ content and solution conductivity when dicofol entered the mass spectrometer. Density functional theory can be used to analyze and interpret the mechanism of dicofol fragmentation reaction in ESI source. Dicofol reduced the molecular energy from 8.8 ± 0.05 kcal/mol to 1.0 ± 0.05 kcal/mol, indicating that the internal energy release from high to low was the key driving force of in-source fragmentation. A method based on HPLC-MS/MS was developed to analyze dicofol residues in environmental water. The LOQ was 0.1 μg/L, which was better than the previous GC or GC-MS methods. This study not only proposed an HPLC-MS/MS analysis method for dicofol for the first time but also explained the in-source fragmentation mechanism of compounds in ESI source, which has positive significance for the study of compounds with unconventional mass spectrometry behavior in the field of organic pollutant analysis and metabonomics.
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Affiliation(s)
- Jun Xie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yage Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongqiang Ma
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lizhen Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Bernardo-Bermejo S, Xue J, Hoang L, Billings E, Webb B, Honders MW, Venneker S, Heijs B, Castro-Puyana M, Marina ML, van den Akker EB, Griffioen M, Siuzdak G, Giera M, Sánchez-López E. Quantitative multiple fragment monitoring with enhanced in-source fragmentation/annotation mass spectrometry. Nat Protoc 2023; 18:1296-1315. [PMID: 36755131 PMCID: PMC10364092 DOI: 10.1038/s41596-023-00803-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/19/2022] [Indexed: 02/10/2023]
Abstract
Analytical techniques with high sensitivity and selectivity are essential to the quantitative analysis of clinical samples. Liquid chromatography coupled to tandem mass spectrometry is the gold standard in clinical chemistry. However, tandem mass spectrometers come at high capital expenditure and maintenance costs. We recently showed that it is possible to generate very similar results using a much simpler single mass spectrometry detector by performing enhanced in-source fragmentation/annotation (EISA) combined with correlated ion monitoring. Here we provide a step-by-step protocol for optimizing the analytical conditions for EISA, so anyone properly trained in liquid chromatography-mass spectrometry can follow and apply this technique for any given analyte. We exemplify the approach by using 2-hydroxyglutarate (2-HG) which is a clinically relevant metabolite whose D-enantiomer is considered an 'oncometabolite', characteristic of cancers associated with mutated isocitrate dehydrogenases 1 or 2 (IDH1/2). We include procedures for determining quantitative robustness, and show results of these relating to the analysis of DL-2-hydroxyglutarate in cells, as well as in serum samples from patients with acute myeloid leukemia that contain the IDH1/2 mutation. This EISA-mass spectrometry protocol is a broadly applicable and low-cost approach for the quantification of small molecules that has been developed to work well for both single-quadrupole and time-of-flight mass analyzers.
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Affiliation(s)
- Samuel Bernardo-Bermejo
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Alcalá de Henares (Madrid), Spain
| | - Jingchuan Xue
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, China
| | - Linh Hoang
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth Billings
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA
| | - Bill Webb
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA
| | - M Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sanne Venneker
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - María Castro-Puyana
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Alcalá de Henares (Madrid), Spain
| | - María Luisa Marina
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Alcalá de Henares (Madrid), Spain
| | - Erik B van den Akker
- Center for Computational Biology, Leiden University Medical Center, Leiden, the Netherlands.,The Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.,Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA, USA.
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
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