Table 1.
Glycoproteins identified in FFPE lung and frozen lung, with their corresponding peak intensity detected by MS.
| IPI | protein name | Peptide | cellular locatin |
P* | tryptic Ends |
FFPE lung | FrozenLung | ratio # |
|---|---|---|---|---|---|---|---|---|
| Category I proteins identified in both FFPE lung and frozen lung | ||||||||
| IPI00108041 | Stromal interaction molecule 1 | R.LAVTN*TTM#TGTVLK.M | TM | 1 | 2 | 36.7±22.9 | 93.0±5.8 | 2.5 |
| IPI00111013 | Cathepsin D | K.YYHGELSYLN*VTR.K | S | 1 | 2 | 93.7±0.1 | 149.8±10.3 | 1.6 |
| IPI00113539 | Fibronectin | R.DQCIVDDITYNVN*DTFHK.R | S | 1 | 2 | 29.0±2.1 | 163.5±57.8 | 5.7 |
| IPI00114958 | Splice Isoform HMW of Kininogen-1 | K.HSIEHFNN*NTDHSHLF.T | S | 1 | 2 | 236.0±33.6 | 447.6±78.6 | 1.9 |
| IPI00116913 | Laminin alpha-5 chain | R.LLLGGLPVSGTFHN*FSGCIS.N | S | 1 | 1 | 5.8±0.2 | 15.2±0.7 | 2.6 |
| IPI00117857 | Alpha-1-antitrypsin 1–6 | R.ELVHQSN*TSNIFF.S | S | 0.99 | 2 | 53.6±6.5 | 40.9±4.1 | 0.8 |
| IPI00117957 | Asporin | R.ITDIEN*GTFANIPR.V | S | 1 | 2 | 92.8±25.7 | 26.0±8.7 | 0.3 |
| IPI00121362 | F11r protein | R.AFM#N*SSFTIDPK.S | TM | 1 | 2 | 13.7±6.3 | 63.7±19.7 | 4.7 |
| IPI00122231 | Advanced glycosylation end product-specific receptor | A.QILPN*GSLLLPATGIVDEGTFR.C | TM | 1 | 1 | 32.5±13.3 | 62.7±15.7 | 1.9 |
| IPI00122973 | Splice Isoform 1 of Intercellular adhesion molecule 1 | K.FLFKN*QTLELH.V | TM | 0.97 | 1 | 97.3±34.2 | 45.7±11.3 | 0.5 |
| IPI00123223 | Murinoglobulin-1 | V.M#AQGSIIQTGN*HTHQVEPGEAPVK.G | A | 1 | 2 | 27.2±3.4 | 66.7±2.2 | 2.5 |
| IPI00123831 | SDR1 protein | K.ENGVFEEISN*SSGR.F | TM | 0.99 | 2 | 61.8±5.2 | 59.0±9.0 | 1.0 |
| IPI00125058 | Splice Isoform B of Laminin alpha-3 chain | Q.LLPLGNISDNVDR.I | S | 0.97 | 2 | 50.8±33.8 | 190.7±24.2 | 3.8 |
| IPI00125813 | Dipeptidyl peptidase 4 | K.LDFIVLN*ETR.F | TM | 0.98 | 2 | 13.5±5.7 | 7.1±4.9 | 0.5 |
| IPI00126194 | Alpha-2-macroglobulin | I.SIDTSN*FTAPFLR.V | S | 1 | 2 | 8.4±0.7 | 47.6±5.1 | 5.7 |
| IPI00127352 | AMBP protein | K.KEDSCQLN*YSEGPCLGM#QER.Y | S | 1 | 2 | 53.7±14.8 | 145.6±12.0 | 2.7 |
| IPI00128249 | Alpha-2-HS-glycoprotein | H.ALDPTPLAN*CSVR.Q | S | 1 | 2 | 574.7±76.3 | 1592.0±242.4 | 2.8 |
| IPI00128484 | Hemopexin | R.VAEVEN*GTKPDSDVPEHC.L | S | 0.91 | 1 | 75.9±32.3 | 102.4±50.7 | 1.4 |
| IPI00131830 | Serine protease inhibitor A3K | K.NLINDYVSNQTQGM#IK.E | S | 1 | 2 | 234.0±28.6 | 851.5±242.9 | 3.6 |
| IPI00133751 | Splice Isoform 1 of Microfibrilassociated glycoprotein 4 | R.VDLEDFEN*NTAYAK.Y | S | 0.99 | 2 | 401.5±38.4 | 356.0±29.7 | 0.9 |
| IPI00134585 | Glutamyl aminopeptidase | K.IALN*LTM#YLK.S | TM | 1 | 2 | 5.9±1.3 | 6.2±2.0 | 1.1 |
| IPI00139788 | Serotransferrin | K.N*STLCDLCIGPLK.C | S | 1 | 2 | 37.5±2.2 | 74.2±2.0 | 2.0 |
| IPI00169815 | Procollagen, type VI, alpha 2 | R.GTFTDCALAN*M#TQQIR.Q | S | 0.99 | 2 | 42.9±3.8 | 72.0±4.4 | 1.7 |
| IPI00169896 | Splice Isoform 2 of Choline transporter-like protein 2 | K.TCNPETFPLRN*ESLQCPTAR.C | TM | 1 | 2 | 43.5±16.0 | 45.5±2.6 | 1.1 |
| IPI00273822 | 16 days embryo lung cDNA | K.IGTYEVLN*GSR.L | S | 1 | 2 | 25.6±6.0 | 49.7±6.2 | 1.9 |
| IPI00322447 | RA175 | R.FQLLN*FSSSELK.V | TM | 1 | 2 | 12.3±2.1 | 13.5±2.2 | 1.1 |
| IPI00331214 | Platelet glycoprotein IV | K.VISNN*CTSYGVLDIGK.C | TM | 0.98 | 2 | 49.0±15.6 | 224.9±12.0 | 4.6 |
| IPI00345112 | IntegrIn alpha 8 | R.M#VVCDLGNPM#VTGTN*FSLGLR.F | TM | 1 | 2 | 21.9±1.7 | 15.7±2.0 | 0.7 |
| IPI00406434 | Mini-agrin | K.NELM#LN*SSLM#R.I | S | 1 | 2 | 93.6±29.7 | 228.5±7.1 | 2.4 |
| IPI00466371 | 16 days neonate cerebellum cDNA, | R.GELQSEN*SSLTLSSSNR.K | TM | 0.98 | 2 | 63.4±9.0 | 110.4±19.8 | 1.7 |
| IPI00467944 | 61 kDa protein | L.DLGGASTQITFVPQN*STIESPENSLQFR.L | TM | 1 | 1 | 12.8±1.0 | 56.3±1.4 | 4.4 |
| Categroy II proteins identified only in frozen lung | ||||||||
| IPI00113797 | Napsin A | W.FN*LTGQDYVIK.I | S | 0.96 | 1 | 333.5±32.5 | 191.0±24.0 | 0.6 |
| IPI00113824 | Basement membrane-specific heparan sulfate proteoglycan core protein | R.SLTQGSLIVGNLAPVN*GTSQGK.F | A | 1 | 2 | 4.1±0.1 | 40.0±1.2 | 9.8 |
| IPI00113869 | Splice Isoform 2 of Basigin | W.FKTSDTGEEEAITN*STEANGK.Y | A | 0.99 | 2 | 30.2±29.6 | 19.9±4.7 | 0.7 |
| IPI00115516 | EMILIN-1 | R.LEDRFN*STLGPSEEQEK.N | S | 0.99 | 2 | 33.8±5.3 | 110.4±14.1 | 3.3 |
| IPI00116105 | Corticosteroid-binding globulin | M.M#VQSGN*ISYFR.D | S | 1 | 2 | 161.9±25.4 | 90.0±8.2 | 0.6 |
| IPI00117093 | Laminin beta-3 chain | R.QTACTPGDCPGELCPQDN*GTACGSHCR.G | A | 1 | 2 | 35.2±2.3 | 38.8±6.2 | 1.1 |
| IPI00123957 | Cd97 protein | R.DFNPATVN*YTIQK.L | TM | 1 | 2 | 38.9±27.9 | 111.7±9.5 | 2.9 |
| IPI00126050 | Bone marrow macrophage cDNA, RIKEN full-length enriched library | K.EVM#NLLQPLN*VTK.V | S | 0.94 | 2 | 167.8±22.3 | 877.8±119.4 | 5.2 |
| IPI00132474 | Integrin beta-1 | K.SAVGTLSGN*SSNVI.Q | TM | 0.96 | 1 | 67.5±22.8 | 403.2±99.5 | 6.0 |
| IPI00272381 | 2 days neonate sympathetic ganglion cDNA | K.DM#SDGFISN*LTIQR.Q | S | 1 | 2 | 45.5±2.8 | N/A | |
| IPI00272690 | Angiotensin-converting enzyme, somatic isoform | K.TFDVSN*FQN*SSIKR.I | TM | 1 | 2 | 177.1±64.9 | 177.5±15.5 | 1.0 |
| IPI00420955 | Sortilin 1 | K.DITNLIN*NTFIR.T | TM | 0.92 | 2 | 6.2±0.1 | 9.7±1.9 | 1.6 |
| IPI00469123 | Melanoma cell adhesion molecule | N.SLGSN*TTTIVLK.L | TM | 0.98 | 1 | 169.5±21.3 | 105.2±13.6 | 0.6 |
| IPI00649550 | Protein | E.KQELSEYN*ATAIK.S | TM | 1 | 1 | 29.7±4.7 | 76.7±18.5 | 2.6 |
| Category III proteins identified only in FFPE lung | ||||||||
| IPI00330833 | Complement C5 | F.VLNLPSN*VTVLK.F | S | 0.99 | 2 | 21.3±3.5 | 0.0 | |
| IPI00417180 | UDP glycosyltransferase 1 family, polypeptide A10 | K.EFEAYVN*ASGEHGI.V | TM | 1 | 1 | 529.5±77.6 | 324.1±22.0 | 0.6 |
*
probability score of peptides by ProteinProphet
#
ratio of peptide intensity from frozen lung vs. FFPE lung