Quantitative multiple fragment monitoring with enhanced in-source fragmentation/annotation mass spectrometry

Gary Siuzdak, Samuel Bernardo-Bermejo, Jingchuan Xue, Linh Hoang, Elizabeth Billings, Bill Webb, M. Willy Honders, Sanne Venneker, Bram Heijs, María Castro-Puyana, María Luisa Marina, Erik B. van den Akker, Marieke Griffioen, Martin Giera, Elena Sánchez-López

Published: 2023-02-07 DOI: 10.1038/s41596-023-00803-0

Mass spectrometry

EISA

Quantitative analysis

Clinical samples

2-Hydroxyglutarate

AI 解读

Supplementary information

Supplementary Information

Supplementary Procedure and Figs. 1–5.

Reporting Summary

Purification of infection-associated macropinosomes by magnetic isolation for proteomic characterization

Hi-CO: 3D genome structure analysis with nucleosome resolution

Practical and concise synthesis of nucleoside analogs

Comprehensive analysis of glycosphingolipid glycans by lectin microarrays and MALDI-TOF mass spectrometry

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal–assisted labeling

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools

Capture of the newly transcribed RNA interactome using click chemistry

Design, assembly, and characterization of membrane-spanning DNA nanopores

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq

查看全部

Sections

Figures

References

Supplementary information

Holcapek, M., Jirasko, R. & Lisa, M. Recent developments in liquid chromatography–mass spectrometry and related techniques. J. Chromatogr. A. 1259, 3–15 (2012).
Leung, K. S.-Y. & Fong, B. M.-W. LC–MS/MS in the routine clinical laboratory: has its time come? Anal. Bioanal. Chem. 406, 2289–2301 (2014).
Wishart, D. Emerging applications of metabolomics in drug discovery and precision medicine. Nat. Rev. Drug. Discov. 15, 473–484 (2016).
Blaženović, I., Kind, T., Ji, J. & Fiehn, O. Software tools and approaches for compound identification of LC–MS/MS data in metabolomics. Metabolites 8, 31 (2018).
Xue, J. et al. Enhanced in-source fragmentation annotation enables novel data independent acquisition and autonomous METLIN molecular identification. Anal. Chem. 92, 6051–6059 (2020).
Xue, J. et al. Single quadrupole multiple fragment ion monitoring quantitative mass spectrometry. Anal. Chem. 93, 10879–10889 (2021).
Xue, J., Derks, R. J. E., Hoang, L., Giera, M. & Siuzdak, G. Proteomics with enhanced in-source fragmentation/annotation: applying XCMS–EISA Informatics and Q-MRM high-sensitivity quantification. J. Am. Soc. Mass Spectrom. 32, 2644–2654 (2021).
Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739–743 (2009).
Struys, E. A., Jansen, E. E. W., Verhoeven, N. M. & Jakobs, C. Measurement of urinary d- and l-2-hydroxyglutarate enantiomers by stable-isotope-dilution liquid chromatography-tandem mass spectrometry after derivatization with diacetyl-l-tartaric anhydride. Clin. Chem. 50, 1391–1395 (2004).
Zhou, J. & Yin, Y. Strategies for large-scale targeted metabolomics quantification by liquid chromatography–mass spectrometry. Analyst 141, 6362 (2016).
González-Ruiz, V., Olives, A. I. & Martin, M. A. Core-shell particles lead the way to renewing high-performance liquid chromatography. TrAC-Trend Anal. Chem. 64, 17–28 (2015).
Ciccimaro, E. & Blair, I. A. Stable-isotope dilution LC–MS for quantitative biomarker analysis. Bioanalysis 2, 311–341 (2010).
González, A. G., Herrador, M. A. & Asuero, A. G. Intra-laboratory assessment of method accuracy (trueness and precision) by using validation standards. Talanta 82, 1995–1998 (2010).
Pansuriya, T. C. et al. Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome. Nat. Genet. 43, 1256–1261 (2011).
Gil-Benso, R. et al. Establishment and characterization of a continuous human chondrosarcoma cell line, ch-2879: comparative histologic and genetic studies with its tumor of origin. Lab. Invest. 83, 877–887 (2003).
Scully, S. P. et al. Marshall Urist Award. Interstitial collagenase gene expression correlates with in vitro invasion in human chondrosarcoma. Clin. Orthop. Relat. Res. 376, 291–303 (2000).
Arindrarto, W. et al. Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing. Leukemia 35, 47–61 (2021).
Oldham, W. M. & Loscalzo, J. Quantification of 2-hydroxyglutarate enantiomers by liquid chromatography-mass spectrometry. Bio. Protoc. 20, e1908 (2016).
Gu, H., Liu, G., Wang, J., Aubry, A.-F. & Arnold, M. E. Selecting the correct weighting factors for linear and quadratic calibration curves with least-squares regression algorithm in bioanalytical LC–MS/MS assays and impacts of using incorrect weighting factors on curve stability, data quality, and assay performance. Anal. Chem. 86, 8959–8966 (2014).
Analytical Procedures and Methods Validation (US Food and Drug Administration, 2000).
Kranendijk, M., Struys, E. A., Salomons, G. S., Van der Knaap, M. S. & Jakobs, C. Progress in understanding 2-hydroxyglutaric acidurias. J. Inherit. Metab. Dis. 35, 571–587 (2012).

Quantitative multiple fragment monitoring with enhanced in-source fragmentation/annotation mass spectrometry

Supplementary information

推荐阅读