SUPPORTING INFORMATION. Multimodal Mass Spectrometry Imaging of N-glycans and Proteins from the Same

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1 SUPPORTING INFORMATION Multimodal Mass Spectrometry Imaging of N-glycans and Proteins from the Same Tissue Section. Bram Heijs 1, Stephanie Holst 1, Inge H. Briaire-de Bruijn 2, Gabi W. van Pelt 3, Arnoud H. de Ru 1, Peter A. van Veelen 1, Richard R. Drake 4, Anand S. Mehta 5, Wilma E. Mesker 3, Rob A. Tollenaar 3, Judith V.M.G. Bovée 2, Manfred Wuhrer 1, Liam A. McDonnell 1,2,6* 1 Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands. 2 Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands. 3 Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands. 4 Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA. 5 Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA. 6 Fondazione Pisana per la Scienza ONLUS, Pisa, Italy. * Corresponding author and reprint requests Dr. Liam A. McDonnell, Center for Proteomics and Metabolomics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; L.A.Mcdonnell@lumc.nl; Phone: ; Fax: S-1

2 Table of content Figure S-1: Annotated histological images.. S-3 Figure S-2: MALDI-TOF-MS and MALDI-FTICR-MS methods... S-5 Figure S-3: Comparison of N-glycan analyses of LMS-1 and LMS-2. S-6 Figure S-4: N-glycan MALDI-MSI results for CRC and MLS. S-7 Figure S-5: Comparison of proteolytic peptide analyses of LMS-1 and LMS-2. S-9 Figure S-6: Analysis of proteolytic fragments from CRC and MLS by MALDI-MSI... S-10 Figure S-7: Comparisons of control and sequential digestion matrix proteomes... S-12 Figure S-8: Protein sequence coverage in LG3BP_HUMAN and VIME_HUMAN. S-13 Supplementary file: Supporting_Information_Sequential_OTD_MSI_S-9 S-2

3 Figure S-1 Annotated histological images S-3

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5 Figure S-2 MALDI-TOF-MS and MALDI-FTICR-MS methods (A) An overview of important parameters in the MALDI-TOF-MS method used to obtain N- glycan MALDI-MSI data. (B) An overview of important parameters in the MALDI-FTICR- MS method used to obtain MALDI-MSI data on proteolytic peptides. A - Bruker UltrafleXtreme Parameter Value Laser power 70 % Laser shots per pixel 500 Laser focus setting 3_medium Laser frequency 2000 Hz Ion Source 1 voltage 25.0 kv Ion Source 2 voltage 22.5 kv Lens voltage 8.5 kv Reflector 1 voltage kv Reflector 2 voltage kv (50.8 % refl) Matrix suppression Deflection up to 890 Da B - Bruker SolariX XR (9.4T) Parameter Value Laser power 35 % Laser shots per pixel 150 Laser focus setting Minimum Laser frequency 2000 Hz Source optics plate offset voltage V Source optics deflector plate voltage V Source optics capillary exit voltage V Source optics funnel 1 voltage V Source optics skimmer 1 voltage 18.0 V Source optics funnel RF amplitude Vpp Octopole frequency 5 MHz Octopole RF amplitude Vpp Quadrupole Q1 mass 1000 m/z Collision cell collision voltage -2.0 V Collision cell DC Extract bias 0.5 V Collision cell RF frequency 2 MHz Collision cell collision RF amplitude Vpp Transfer optics time of flight 1.7 ms Transfer optics frequency 2 MHz Transfer optics RF amplitude Vpp Para Cell transfer exit lens voltage V Para Cell analyzer entrance voltage V Para Cell side kick voltage 0.0 V Para Cell side kick offset voltage 0.0 V Para Cell front trap plate voltage 1.5 V Para Cell back trap plate voltage 1.5 V Para Cell back trap plate quench voltage V Para Cell sweep excitation power percentage 45.0 % S-5

6 Figure S-3 Comparison of N-glycan analyses of LMS-1 and LMS-2 (A) A comparison of the overall average spectra obtained from the LMS-1 (L1091-3, black) and, the duplicate, LMS-2 (L1091-3, grey) tissue sections during N-glycan MALDI-MSI. (B) Visualizations of the distribution of various N-glycans throughout the LMS-1 and LMS-2 tissues. The annotated glycan structures represent compositions which were either confirmed by MS/MS identification or were known from literature, but structural isomers cannot be excluded. The images were obtained from TIC normalized datasets. S-6

7 Figure S-4 N-glycan MALDI-MSI results for CRC and MLS (A) The overall average mass spectrum after the N-glycan MALDI-MSI analysis of the CRC (C67) tissue. (B) Scanned image of the H&E stained CRC (C67) tissue. (C) Visualizations of the distribution of various N-glycans throughout the tissue. The images were obtained from a TIC normalized dataset. (D) The overall average mass spectrum after the N-glycan MALDI- MSI analysis of the MLS tissue (L2039). (E) Scanned image of the H&E stained MLS (L2039) tissue. (F) Visualizations of the distribution of various N-glycans throughout the tissue. The annotated glycan structures represent compositions which were either confirmed by MS/MS identification or were known from literature, but structural isomers cannot be excluded. The images were obtained from a TIC normalized dataset. S-7

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9 Figure S-5 Comparison of proteolytic peptide analyses of LMS-1 and LMS-2 (A) A comparison of the overall average spectra obtained from the LMS-1 (L1091-3, black) and, the duplicate, LMS-2 (L1091-3, grey) tissue sections during MALDI-MSI analysis of proteolytic peptides. (B) Comparison of the visualizations of specific peptide distributions in both duplicate LMS analyses. The peptides were confirmed to be present in the MALDImatrix by LC-MS/MS of extracts and were assigned to the MALDI-FTICR-MSI datasets with an error < 10 ppm. The images were obtained from a RMS normalized datasets. S-9

10 Figure S-6 Analysis of proteolytic fragments from CRC and MLS by MALDI-MSI (A) A comparison of the profiles of MALDI-FTICR-MSI overall average spectra obtained after both sequential trypsin digestion (top, black) and control trypsin digestion (bottom, grey) of the CRC (C67) tissue. (B) Scanned image of the H&E stained CRC (C67) tissue. (C) Comparison of the visualizations of specific peptide distributions. (D) A comparison of the profiles of MALDI-FTICR-MSI overall average spectra obtained after both sequential trypsin digestion (top, black) and control trypsin digestion (bottom, grey) of the MLS (L2039) tissue. (E) Scanned image of the H&E stained MLS (L2039) tissue. (F) Comparison of the visualizations of specific peptide distributions. Unless indicated otherwise, the peptides were confirmed to be present in the MALDI-matrix by LC-MS/MS of extracts and were assigned to the MALDI-FTICR-MSI datasets with an error < 10 ppm. The images were obtained from a RMS normalized datasets. S-10

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12 Figure S-7 Comparisons of control and sequential digestion matrix proteomes Venn diagrams showing the differences and overlap between (A) the number of protein identifications in both control and sequential digestions, and (B) the differences in the number of identified peptides per protein. The numbers in (B) represent the number of proteins. In blue, the number of proteins for which the number of peptides in the control digestion was larger than in the sequential digestion. In red, the number of proteins for which the number of peptides was higher in the sequential digestion than in the control digestion. The overlapping part represents the proteins where the number of peptides was equal between control and sequential digestions. S-12

13 Figure S-8 Protein sequence coverage in LG3BP_HUMAN and VIME_HUMAN The amino acid sequences of both galectin-3 binding protein and vimentin. The identified peptides have been annotated to indicate the sequence coverage in the different experiments. Galectin-3 Binding Protein (LG3BP_HUMAN) amino acid sequence LG3BP_HUMAN MTPPRLFWVW LLVAGTQGVN DGDMRLADGG ATNQGRVEIF YRGQWGTVCD NLWDLTDASV LG3BP_HUMAN LG3BP_HUMAN LMS_control LMS_sequential CRC_sequential LG3BP_HUMAN LG3BP_HUMAN LG3BP_HUMAN LMS_control LMS_sequential CRC_sequential VCRALGFENA TQALGRAAFG QGSGPIMLDE VQCTGTEASL ADCKSLGWLK SNCRHERDAG VVCTNETRST HTLDLSRELS EALGQIFDSQ RGCDLSISVN VQGEDALGFC GHTVILTANL ELS EALGQIFDSQ R ELS EALGQIFDSQ R EAQALWKEPG SNVTMSVDAE CVPMVRDLLR YFYSRRIDIT LSSVKCFHKL ASAYGARQLQ GYCASLFAIL LPQDPSFQMP LDLYAYAVAT GDALLEKLCL QFLAWNFEAL TQAEAWPSVP TDLLQLLLPR SDLAVPSELA LLKAVDTWSW GERASHEEVE GLVEKIRFPM MLPEELFELQ SDLAVPSELA LLKAVDTWSW GER SDLAVPSELA LLKAVDTWSW GER LG3BP_HUMAN FNLSLYWSHE ALFQKKTLQA LEFHTVPFQL LARYKGLNLT EDTYKPRIYT SPTWSAFVTD LMS_control LMS_sequential TLQA LEFHTVPFQL LAR IYT SPTWSAFVTD CRC_sequential TLQA LEFHTVPFQL LAR GLNLT EDTYKPRIYT SPTWSAFVTD LG3BP_HUMAN SSWSARKSQL VYQSRRGPLV KYSSDYFQAP SDYRYYPYQS FQTPQHPSFL FQDKRVSWSL LMS_control LMS_sequential SSWSAR CRC_sequential SSWSARK LG3BP_HUMAN VYLPTIQSCW NYGFSCSSDE LPVLGLTKSG GSDRTIAYEN KALMLCEGLF VADVTDFEGW LG3BP_HUMAN KAAIPSALDT NSSKSTSSFP CPAGHFNGFR TVIRPFYLTN SSGVD LMS_control LMS_sequential TVIRPFYLTN SSGVD CRC_sequential AAIPSALDT NSSK TVIRPFYLTN SSGVD S-13

14 VIME_HUMAN LMS_control LMS_sequential CRC_sequential Vimentin (VIME_HUMAN) amino acid sequence MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV SLYASSPGGV SLYASSPGGV SLYASSPGGV SLYASSPGGV VIME_HUMAN YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK LMS_control YATR VELQEL NDR LMS_sequential YATR LL QDSVDFSLAD AINTEFKNTR VELQEL NDR YATR LL QDSVDFSLAD AINTEFKNTR CRC_sequential YATR LL QDSVDFSLAD AINTEFKNTR VELQEL NDR VIME_HUMAN VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE LMS_control LGDLY EEEMR DNLAE LMS_sequential FLEQQNKI LLAELEQLKG QGK LGDLY EEEMR DNLAE LGDLY EEEMR CRC_sequential FLEQQNKI LLAELEQLKG QGK LGDLY EEEMR DNLAE VIME_HUMAN DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE LMS_control DIMR LQ EEMLQREEAE NTLQSFRQDV DNASLAR LMS_sequential DIMR LQ EEMLQREEAE NTLQSFRQDV DNASLAR VESLQEE IAFLKK EEAE NTLQSFR CRC_sequential DIMR EEAE NTLQSFR VIME_HUMAN LMS_control LMS_sequential CRC_sequential EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE NLQEAEEW YKSKFADLSE NLQEAEEW YKSKFADLSE NLQEAEEW YKSKFADLSE NLQEAEEW YKSKFADLSE VIME_HUMAN AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD LMS_control AANR EMEEN FAVEAANYQD LMS_sequential AANR EMEEN FAVEAANYQD AANR CRC_sequential AANR EMEEN FAVEAANYQD VIME_HUMAN TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS LMS_control TIGR ISLPLPNFSS LMS_sequential TIGR ISLPLPNFSS ISLPLPNFSS CRC_sequential TIGR ISLPLPNFSS VIME_HUMAN LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE LMS_control LNLRETNLDS LPLVDTHSK DGQVINETSQ HHDDLE LMS_sequential LNLRETNLDS LPLVDTHSK DGQVINETSQ HHDDLE LNLRETNLDS LPLVDTHSK DGQVINETSQ HHDDLE CRC_sequential LNLRETNLDS LPLVDTHSK DGQVINETSQ HHDDLE S-14