Supporting Information for MassyTools-assisted data analysis of total serum N-glycome changes associated with pregnancy

Transcription

1 Supporting Information for MassyTools-assisted data analysis of total serum N-glycome changes associated with pregnancy Bas C. Jansen 1, Albert Bondt 1,2, Karli R. Reiding 1, Coen J. de Jong 1, David Falck 1, Radboud J.E.M. Dolhain 2, Yoann Rombouts 1,3,4, Manfred Wuhrer 1,5 1 Center for Proteomics and Metabolomics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands 2 Department of Rheumatology, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands 3 Department of Rheumatology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands 4 Centre National de la Recherche Scientifique, UMR 8576, Villeneuve d'ascq, France 5 Division of BioAnalytical Chemistry, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands Corresponding author: Manfred Wuhrer, m.wuhrer@lumc.nl, Tel Running title: MassyTools: A tool for automated quantitation and quality control of glycoproteomics MALDI-MS data Table of Contents Supporting Information, Figures (Word File) Supporting Information, Figure S-1. Isotopic quality criteria... S-2 Supporting Information, Figure S-2. Reference TPNG spectrum of healthy volunteers... S-3 Supporting Information, Figure S-3. mab1 calibration... S-5 Supporting Information, Figure S-4. Cubic spline fit... S-6 Supporting Information, Figure S-5. Background window optimization... S-7 Supporting Information, Figure S-6. mab1 data integration RSD and relative area correlation... S-8 Supporting Information, Figure. S-7. TPNG Data Integration with MassyTools... S-9 References... S-10 Supporting Information, Tables (Excel File) Supporting Information, Table S-1. Overview of the building blocks available in the current release of MassyTools... Tab 1 Supporting Information, Table S-2. Parameters that can be changed in MassyTools, including their default values.... Tab 2 Supporting Information, Table S-3. Post calibration mass errors for all mab1 glycans and glycopeptides... Tab 3 Supporting Information, Table S-4. Post calibration mass errors for the TPNG analytes... Tab 7 Supporting Information, Table S-5. Post calibration mass error of selected analytes using a spline fit, APEX and Bruker Data Analysis peak picked accurate mass.... Tab 11 Supporting Information, Table S-6. Comparison between integration quality using mab1 glycan and glycopeptide samples... Tab 12 Supporting Information, Table S-7. TPNG integration results, including different curation approaches... Tab 14 S-1

2 Supporting Information, Figure S-1. Isotopic quality criteria. (A) A mass spectrum of a high mannose type N-glycan (Man5, H5N2). (B) Comparison between the theoretical isotopic pattern of H5N2 and the average observed isotopic pattern of H5N2, the observed pattern is taken from the extraction windows marked with a red box. The difference between the theoretical pattern and observed pattern is taken per isotope and used in the QC value calculation. 1 S-2

3 S-3

4 Supporting Information, Figure S-2. Reference TPNG spectrum of healthy volunteers. MALDI-TOF-MS spectrum of ethyl esterified released glycans from TPNG, measured in RP mode. (A) Spectrum from m/z 1, to 2, (B) Spectrum from m/z 2, to 3, (C) Spectrum from m/z 3, to 4, (D) Spectrum from m/z 4, to 5, The displayed spectrum is annotated with all observed glycan structures. For high-mannose and hybrid structures, the proposed structures are based on the synthesis pathway.2 Glycans that are mainly contributed by immunoglobulin G (e.g. H4N3F1) have been well characterized.3 The localization of galactose to the specific antennae cannot be elucidated by MALDI-MS. Glycans that contain an n-acetylhexosamine, additional to the core or LAcNAc units (e.g. H5N5F1S1 and H5N5S1), can either be bisected or contain a truncated antenna. Two of the major plasma glycoproteins, IgA and IgM, are known to contain diantennary bisected glycans.4,5 Antenna fucosylation has been observed on triantennary glycans, for example in α1-acid glycoprotein.6 However, there are other highly abundant glycoproteins with fucosylated trianntenary structures for which the fucose linkage is unknown. Lastly, sialic acid linkages in the spectrum are based on a derivatization technique that creates a unique mass for α2,3-linked and α2,6-linked sialic acids.7 A full list of all compositions that were extracted from this sample can be found in Supporting Information, Table S-5. S-4

5 Supporting Information, Figure S-3. mab1 calibration. Heatplots of the analytes above 1% relative abundance showing the glycan calibrant mass error in ppm post calibration. The natural logarithm of the calibrant signal-to-noise is used for the spot color. (A) Glycan measurements calibrated with a simple flexanalysis method. (B) Glycan measurements calibrated with MassyTools. (C) Glycopeptide measurements calibrated with a simple flexanalysis method. (D) Glycopeptide measurements calibrated with MassyTools. S-5

6 Supporting Information, Figure S-4. Cubic spline fit. (A) MALDI-TOF-MS spectrum region covering the mab1 H5N2 calibrant. (B) MALDI-TOF-MS spectrum region around the mab1 H5N4F1 calibrant. Measured data points are indicated by blue stars, the cubic spline is indicated with a dashed red line. The accurate mass for this calibrant is acquired from the fitted function, marked with a dashed red line. The data point with the highest intensity is marked with a blue line. S-6

7 Supporting Information, Figure S-5. Background window optimization. The average relative standard deviation of a set of glycans as reported with differing m/z ranges for background determination. A range that is too small will detect a background region containing other analytes and/or contaminants, while a range that is too large will underestimate the background area. The optimal RSD values are observed at a window of m/z ± 10. S-7

8 Supporting Information, Figure S-6. mab1 data integration RSD and relative area correlation. (A) Glycan relative area and RSD correlation of all analyte above 0.1% relative abundance. (B) Glycan relative area and RSD correlation of all analytes. (C) Glycopeptide relative area and RSD correlation of all analytes above 0.1% relative abundance. (D) Glycopeptide relative area and RSD correlation of all. MassyTools and a semi-automated method both show an increasing RSD with a decreasing relative area, however the increase with MassyTools is lower. S-8

9 Supporting Information, Figure. S-7. TPNG Data Integration with MassyTools. The average relative area and standard deviation for the 35 most abundant analytes in total plasma N-glycome as measured in 24 MALDI-TOF-MS spectra of healthy standards. The most abundant peak (H5N4E2) shows a relative standard deviation (RSD) of 5.8%. S-9

10 References 1. Nicolardi, S.; Palmblad, M.; Dalebout, H.; Bladergroen, M.; Tollenaar, R. E. M.; Deelder, A.; van der Burgt, Y. M. Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling. J. Am. Soc. Mass Spectrom. 2010, 21(9) Kornfeld, R.; Kornfeld, S. Assembly of asparagine-linked oligosaccharides. Annu Rev Biochem 1985, Fujii, S.; Nishiura, T.; Nishikawa, A.; Miura, R.; Taniguchi, N. Structural heterogeneity of sugar chains in immunoglobulin G. Conformation of immunoglobulin G molecule and substrate specificities of glycosyltransferases. J Biol Chem 1990, 265(11) Arnold, J. N.; Wormald, M. R.; Suter, D. M.; Radcliffe, C. M.; Harvey, D. J.; Dwek, R. A.; Rudd, P. M.; Sim, R. B. Human Serum IgM Glycosylation: IDENTIFICATION OF GLYCOFORMS THAT CAN BIND TO MANNAN-BINDING LECTIN. Journal of Biological Chemistry 2005, 280(32) Mattu, T. S.; Pleass, R. J.; Willis, A. C.; Kilian, M.; Wormald, M. R.; Lellouch, A. C.; Rudd, P. M.; Woof, J. M.; Dwek, R. A. The Glycosylation and Structure of Human Serum IgA1, Fab, and Fc Regions and the Role of N-Glycosylation on Fcα Receptor Interactions. Journal of Biological Chemistry 1998, 273(4) Dage, J. L.; Ackermann, B. L.; Halsall, H. B. Site localization of sialyl Lewisx antigen on α1-acid glycoprotein by high performance liquid chromatography-electrospray mass spectrometry. Glycobiology 1998, 8(8) Reiding, K. R.; Blank, D.; Kuijper, D. M.; Deelder, A. M.; Wuhrer, M. High-throughput profiling of protein N-glycosylation by MALDI-TOF-MS employing linkage-specific sialic acid esterification. Anal. Chem. 2014, 86(12) S-10