Self-assembling covalent organic frameworks functionalized. magnetic graphene hydrophilic biocomposite as an ultrasensitive

Size: px

Start display at page:

Download "Self-assembling covalent organic frameworks functionalized. magnetic graphene hydrophilic biocomposite as an ultrasensitive"

Geraldine Watkins
5 years ago
Views:

1 Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2017 Electronic Supporting Information for: Self-assembling covalent organic frameworks functionalized magnetic graphene hydrophilic biocomposite as an ultrasensitive matrix for N-linked glycopeptide recognition Jiaxi Wang, a Jie Li, b Mingxia Gao,* a and Xiangmin Zhang a a Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai , China. b Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, , China. Corresponding author address: mxgao@fudan.edu.cn S-1

2 EXPERIMENTAL SECTION Nano-Liquid chromatography tandem mass spectrometry (Nano-LC MS/MS) analysis of glycopeptides. Glycopeptides enriched from human serum were resuspended with 10 μl solvent A (A: water with 0.1% formic acid; B: ACN with 0.1% formic acid) and then separated by nanolc and analyzed by on-line electrospray tandem mass spectrometry. The experiments were performed on an EASY-nLC 1000 system (Thermo Fisher Scientific, Waltham, MA) connected to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with an online nano-electrospray ion source. 8 μl peptide sample was loaded onto the trap column (Thermo Scientific Acclaim PepMap C18, 100μm x 2cm), with a flow of 10μL/min for 3 min and subsequently separated on the analytical column (Acclaim PepMap C18, 75μm x 25cm) with a linear gradient, from 2% B to 25% B in 105 min. The column was re-equilibrated at initial conditions for 15 min. The column flow rate was maintained at 300 nl/min and column temperature was maintained at 40 C. The electrospray voltage of 2.0 kv versus the inlet of the mass spectrometer was used. The Orbitrap Fusion mass spectrometer was operated in the data-dependent mode to switch automatically between MS and MS/MS acquisition. Survey full-scan MS spectra (m/z ) were acquired in Orbitrap with a mass resolution of at m/z 200. The AGC taget was set to , and the maximum injection time was 50ms. MS/MS acquisition was performed in Orbitrap with 3 s cycle time, the resolution was at m/z 200. The intensity threshold was , and the maximum injection time was 100 ms. The AGC target was set to , and the isolation window was 2 m/z. Ions with charge states 2+, 3+, and 4+ were sequentially fragmented by higher energy collisional dissociation (HCD) with a normalized collision energy (NCE) of 35%, fixed first mass was set at 110. In all cases, one microscan was recorded using dynamic exclusion of 30 seconds. S-2

3 Database search. Tandem mass spectra were extracted by Proteome Discoverer software (Thermo Fisher Scientific, version ). Charge state deconvolution and deisotoping were not performed. All MS/MS samples were analyzed using Mascot (Matrix Science, London, UK; version 2.3.2). The database was the Human UniProtKB/Swiss-Prot database (Release , with sequences). Raw files generated by the Orbitrap Fusion were searched directly using a 10ppm precursor mass tolerance and a 50 mmu fragment mass tolerance. The enzyme specificity with trypsin was used. Up to two missed cleavages were allowed and peptides with at least 7 amino acids were retained. Carbamidomethyl on cysteine was set as a fixed modification. Oxidation on methionine and Deamidation on asparagine were set as variable modifications. Use the percolator algorithm to control peptide level false discovery rates (FDR) lower than 1%. The Asn modification that did not occur in the N-X- S/T (X P) sequon was eliminated to ensure the false positive rate below 1% for the identified glycosylation sites. S-3

4 Fig. S1 Schematic representation for the direct construction of COF-5. S-4

5 Fig. S2 The extended structures based on the eclipsed arrangements. C, gray; O, orange; B, blue. H atoms are omitted for clarity. S-5

6 Fig. S3 The TEM images of (a, b) COF-5 materials, (c) and (d) biocomposite. S-6

7 Fig. S4 The energy dispersive X-ray (EDX) spectrum data of biocomposite. S-7

Fig. S5 The photos of the aqueous dispersion of MagG@COF-5

8 Fig. S5 The photos of the aqueous dispersion of biocomposite: (a) before and (b) after separation by a magnet for 5 seconds. S-8

9 Fig. S6 TGA curves of magg and biocomposite. S-9

10 Fig. S7 N 2 adsorption/desorption isotherms of (a) magg and (b) MagG@COF-5 biocomposite. S-10

11 Fig. S8 MALDI-TOF-MS analysis of peptides derived from HRP enriched by 5 biocomposite with different buffer solution (a) ACN/H 2 O/TFA (95:4:1, v/v/v); (b) ACN/H 2 O/TFA (95:4.9:0.1, v/v/v); (c) ACN/H 2 O/TFA (85:14:1, v/v/v) and (d) ACN/H 2 O/TFA (85:14.9:0.1, v/v/v). S-11

Fig. S9 The effect of enrichment time and different quantity of the MagG@COF-5 biocomposite in

12 Fig. S9 The effect of enrichment time and different quantity of the biocomposite in glycopeptides enriched from 10-6 M HRP tryptic digest (a, b) through three parallel tests. S-12

13 Fig. S10 MALDI-TOF-MS for the glycopeptides derived from HRP tryptic digest: (a) after treatment with biocomposite used for the first time, (b) after enrichment with recycled 2 times, (c) 3 times, (d) 4 times and (e) 5 times. S-13

14 Fig. S11 MALDI-TOF-MS for the glycopeptides derived from HRP tryptic digest: (a) after treatment with the biocomposite for the first time and (b) after enrichment with the which had been placed for one month. S-14

15 Table S1. Detailed information of the observed glycopeptides in HRP tryptic digest. N# denotes the N-linked glycosylation site. No. Observed m/z Glycan composition Amino acid sequence XylMan3GlcNAc2 PN#VSNIVR Man2GlcNAc2 MGN#ITPLTGTQGQIR XylMan3FucGlcNAc2 SSPN#ATDTIPLVR XylMan3GlcNAc2 MGN#ITPLTGTQGQIR FucGlcNAc GLIQSDQELFSSPN#ATDTIPLVR XylMan2GlcNAc2 SFAN#STQTFFNAFVEAMDR XylMan3FucGlcNAc2 GLCPLNGN#LSALVDFDLR XylMan3FucGlcNAc2 QLTPTFYDNSCPN#VSNIVR XylMan3FucGlcNAc2 SFAN#STQTFFNAFVEAMDR XylMan3FucGlcNAc2 NQCRGLCPLNGN#LSALVDFDLR XylMan3FucGlcNAc2 GLIQSDQELFSSPN#ATDTIPLVR XylMan3FucGlcNAc2 LHFHDCFVNGCDASILLDN#TTSFR XylMan3GlcNAc2 QLTPTFYDNSC(AAVESACPR)PN#VSNIVR-H2O XylMan3FucGlcNAc2 QLTPTFYDNSC(AAVESACPR)PN#VSNIVR XylMan3FucGlcNAc2, XylMan3GlcNAc2 XylMan3FucGlcNAc2, XylMan3FucGlcNAc2 LYN#FSNTGLPDPTLN#TTYLQTLR LYN#FSNTGLPDPTLN#TTYLQTLR S-15

16 Table S2. Data of the identified N-linked glycopeptides enriched by biocomposite. N# denotes the N-linked glycosylation site. No. Sequence Protein Group Charge MH+ [Da] Accessions 1 GNEANYYSN#ATTDEHGLVQFSIN#TTNVMGTSLTVR P LAGKPTHVN#VSVVMAEVDGTcY P STGKPTLYN#VSLVMSDTAGTcY P QQQHLFGSN#VTDcSGNFcLFR P ITYSIVQTN#cSK P NLFLNHSEN#ATAK P FEVDSPVYN#ATWSASLK P ELHHLQEQN#VSNAFLDKGEFYIGSK P ELHHLQEQN#VSNAFLDK P TKPREEQYN#STYR P TKPREEQFN#STFR P LGSFEGLVN#LTFIHLQHNR P KLPPGLLAN#FTLLR P NAHGEEKEN#LTAR Q VGQLQLSHN#LSLVILVPQNLK P VYKPSAGN#nSLYR P TVLTPATnHMGN#VTFTIPANR P YPHKPEIN#STTHPGADLQENFcR P FSDGLESN#SSTQFEVK P0C0L FSDGLESN#SSTQFEVKK P0C0L VYKPSAGN#NSLYR P KLHINHNN#LTESVGPLPK P VTQVYAEN#GTVLQGSTVASVYK P LPPGLLAN#FTLLR P LLDLSGNN#LTHLPK P NPPMGGnVVIFDTVITNQEEPYQN#HSGR P EHEAQSN#ASLDVFLGHTnVEELMK P SLPNFPN#TSATAN#ATGGR Q6UXB QLAHQSN#STnIFFSPVSIATAFAmLSLGTK P DIVEYYN#DSN#GSHVLQGR P GLTFQQN#ASSmcVPDQDTAIR P QVFPGLnYcTSGAYSN#ASSTDSASYYPLTGDTR P SWPAVGN#cSSALR P ALPQPQN#VTSLLGcTH P GLTFQQN#ASSMcVPDQDTAIR P LSDLSIN#STEcLHVHcR P LQNNENN#IScVER Q FVEGSHN#STVSLTTK P QLAHQSN#STNIFFSPVSIATAFAMLSLGTK P KKEDALN#ETR P YAEDKFN#ETTEK P LHINHNN#LTESVGPLPK P IYSGILN#LSDITK P S-16

17 44 DKMFSQN#DTR P DFYVDEN#TTVR P EHEAQSN#ASLDVFLGHTNVEELMK P QVHFFVN#ASDVDNVK Q96IY LYLGSnN#LTALHPALFQN#LSK P LQNNEnN#IScVER Q MVSHHN#LTTGATLINEQWLLTTAKNLFLN#HSEnATAK P LYLGSnNLTALHPALFQN#LSK P ADGTVnQIEGEATPVN#LTEPAK P ADGTVnQIEGEATPVN#LTEPAKLEVK P MVSHHN#LTTGATLInEQWLLTTAK P IIVPLnNREN#ISDPTSPLR P GAFISN#FSmTVDGK P MDGASN#VTcInSR P WDPEVN#cSMAQIQLcPPPPQIPNSHN#MTTTLNYR P SLGNVN#FTVSAEALESQELcGTEVPSVPEHGR P SLGNVN#FTVSAEALESQELcGTEVPSVPEHGRK P LQAPLN#YTEFQKPIcLPSK P MVSHHN#LTTGATLINEQWLLTTAK P VVLHPN#YSQVDIGLIK P VVLHPN#YSQVDIGLIKLK P MVSHHN#LTTGATLINEQWLLTTAK P TPLTAN#ITK P SPDVIN#GSPISQK P KEDALN#ETR P GAFISN#FSMTVDGK P LNAENN#ATFYFK P HSHNNN#SSDLHPHK P DIENFN#STQK P ALGFEN#ATQALGR Q LVPHMN#VSAVEK Q96KN GNEAnYYSN#ATTDEHGLVQFSInTTNVMGTSLTVR P NLFLN#HSEN#ATAK P EEQYN#STYRVVSVLTVLHQDWLnGK P EEQFN#STFRVVSVLTVVHQDWLnGK P EGYSN#ISYIVVnHQGISSR P ISEEN#ETTcYMGK P VIDFN#cTTSSVSSALAnTK P VIDFN#cTTSSVSSALANTK P AELSN#HTRPVILVPGcLGNQLEAK P EPGSN#VTMSVDAEcVPMVR Q EEQYN#STYR P EEQYN#STFR P EEQFN#STFR P EEQFN#STFRVVSVLTVVHQDWLNGK P EDALN#ETR P SLTFN#ETYQDISELVYGAK P LPTQN#ITFQTESSVAEQEAEFQSPK Q GVNFN#VSK P S-17

18 93 TMFPN#LTDVR P MFSQN#DTR P DTFVN#ASR P EGYSN#ISYIVVNHQGISSR P SLGnVN#FTVSAEALESQELcGTEVPSVPEHGR P VLSN#nSDANLELINTWVAK P VNQnLVYESGSLN#FSK P THTN#ISESHPN#ATFSAVGEASIcEDDWNSGER P YFYN#GTSmAcETFQYGGcMGnGNNFVTEK P YDFN#SSmLYSTAK P EWDN#TTTEcR P FLNN#GTcTAEGK P YFYN#GTSMAcETFQYGGcmGnGnNFVTEK P YLGN#ATAIFFLPDEGK P YLGN#ATAIFFLPDEGKLQHLENELTHDIITK P YTGN#ASALFILPDQDK P YTGN#ASALFILPDQDKMEEVEAMLLPETLKR P WVSN#KTEGR P AFEN#VTDLQWLILDHNLLENSK P DFVN#ASSK P DFVN#ASSKYEITTIHNLFR P IYSN#HSALESLALIPLQAPLK P VTQN#LTLIEESLTSEFIHDIDR P VLSN#NSDANLELINTWVAK P LQN#LTLPTN#ASIK Q FLnN#GTcTAEGK P YKN#nSDISSTR P GLN#VTLSSTGRnGFK P0C0L LGN#WSAmPScK P TLN#QSSDELQLSmGNAMFVK P VSN#VScQASVSR P LGN#WSAMPScK P VSN#QTLSLFFTVLQDVPVR P GLN#VTLSSTGR P0C0L YKN#NSDISSTR P TLN#QSSDELQLSMGNAMFVK P LAN#LTQGEDQYYLR P GLN#LTEDTYKPR Q AVN#ITSENLIDDVVSLIR P HAN#WTLTPLK P VVN#STTGPGEHLR P VLN#FTTK P FLN#DTMAVYEAK P RNPPMGGNVVIFDTVITNQEEPYQN#HSGR P NPPMGGNVVIFDTVITNQEEPYQN#HSGR P AVLQLNEEGVDTAGSTGVTLN#LTSKPIILR P LnAENN#ATFYFK P FN#SSYLQGTnQITGR P HN#STGcLR P S-18

19 142 QnQcFYN#SSYLNVQR P FN#SSYLQGTNITGR P EN#LTAPGSDSAVFFEQGTTR P FN#LTETSEAEIHQSFQHLLR P AN#LSSQALQMSLDYGFVTPLTSMSIR P EN#ISDPTSPLR P EN#ETEIIK P DN#NSIITR P DN#YTDLVAIQNK P LVLSSEKTVLTPATNHMGN#VTFTIPANR P LSLHRPALEDLLLGSEAN#LTcTLTGLR P ALGISPFHEHAEVVFTAN#DSGPR P LSHNELADSGIPGNSFN#VSSLVELDLSYNK P GGETAQSADPQWEQLnnKN#LSMPLLPADFHK P ADGTVNQIEGEATPVN#LTEPAKLEVK P ADGTVNQIEGEATPVN#LTEPAK P DVQIIVFPEDGIHGFN#FTR P FQSPAGTEALFELHN#ISVADSAN#YScVYVDLKPPFGGSAPSER P SVQEIQATFFYFTPN#KTEDTIFLR P ADTHDEILEGLNFN#LTEIPEAQIHEGFQELLR P LQAILGVPWKDKN#cTSR P VNQNLVYESGSLN#FSK P IYPGVDFGGEELN#VTFVK P LGTSLSSGHVLMN#GTLK P TVLTPATNHMGN#VTFTIPANR P FNPGAESVVLSN#STLK Q SVVAPATDGGLN#LTSTFLR P AALAAFNAQNN#GSNFQLEEISR P QSVPAHFVALN#GSK P LDAPTNLQFVN#ETDSTVLVR P SLDFNTLVDN#ISVDPETGDLWVGcHPnGMK P SRYPHKPEIN#STTHPGADLQENFcR P EHEGAIYPDN#TTDFQR P TVIRPFYLTN#SSGVD Q DIVEYYNDSN#GSHVLQGR P VVAEGFDFAnGINISPDGK P SQILEGLGFN#LTELSESDVHR P IIVPLNNREN#ISDPTSPLR P AQLLQGLGFN#LTER P ngtghgn#sthhgpeymr P ngtghgn#sthhgpeymr P nlfln#hsen#atak P nn#atvheqvggpsltsdlqaqsk P N#TTcQDLQIEVTVK P0C0L N#HScSEGQISIFR O N#GTGHGNSTHHGPEYMR P N#NSDISSTR P N#YTLTGR P N#LSMPLLPADFHK P S-19

20 191 RNPPmGGNVVIFDTVITNQEEPYQN#HSGR P NPPmGGNVVIFDTVITNQEEPYQN#HSGR P TVLTPATNHmGN#VTFTIPANR P mvshhn#lttgatlineqwllttaknlflnhsenatak P mvshhn#lttgatlineqwllttak P mln#tsslleqlneqfnwvsr P VYLQGLIDcYLFGN#SSTVLEDSK P LKELPGVcN#ETMMALWEEcKPcLK P WVLTAAHcLLYPPWDKN#FTENDLLVR P TELFSSScPGGIMLN#ETGQGYQR O DTAVFEcLPQHAMFGN#DTITcTTHGnWTKLPEcR P DTAVFEcLPQHAMFGN#DTITcTTHGnWTK P DTAVFEcLPQHAmFGN#DTITcTTHGnWTK P DAGVVcTN#ETR Q ELPGVcN#ETMMALWEEcKPcLK P LTDTIcGVGN#MSAN#ASDQER P LTDTIcGVGN#mSAnASDQER P AATcINPLN#GSVcERPAN#HSAK O QDQcIYN#TTYLNVQREnGTISR P QDQcIYN#TTYLnVQR P QNQcFYN#SSYLNVQR P LGAcN#DTLQQLMEVFK P LGAcN#DTLQQLMEVFKFDTISEK P DKIcDLLVANNHFAHFFAPQN#LTnMNK P DKIcDLLVANNHFAHFFAPQN#LTNMNK P LGHcPDPVLVNGEFSSSGPVN#VSDK P LGHcPDPVLVnGEFSSSGPVN#VSDK P VTAcHSSQPN#ATLYK P KVScPIMPcSN#ATVPDGEccPR P GIcN#SSDVR O IPcSQPPQIEHGTIN#SSR P KVcQDcPLLAPLN#DTR P GcVLLSYLN#ETVTVSASLESVR P FcRDN#YTDLVAIQNK P IcDLLVANNHFAHFFAPQN#LTNMNK P VcQDcPLLAPLN#DTR P FSLLGHASIScTVEN#ETIGVWRPSPPTcEK P LEPVHLQLQcMSQEQLAQVAAN#ATK Q96PD ciqan#yslmengk P ciqan#yslmengkik P ciqan#yslmengk P csdgwsfdattlddn#gtmlffk P S-20

Improved 6- Plex TMT Quantification Throughput Using a Linear Ion Trap HCD MS 3 Scan Jane M. Liu, 1,2 * Michael J. Sweredoski, 2 Sonja Hess 2 *

Improved 6- Plex TMT Quantification Throughput Using a Linear Ion Trap HCD MS 3 Scan Jane M. Liu, 1,2 * Michael J. Sweredoski, 2 Sonja Hess 2 * 1 Department of Chemistry, Pomona College, Claremont, California