BCE-ECM was harvested by adding lysis buffer (7 M urea, 2 M thiourea, 4% CHAPS, 0.2% ampholytes [BioLytes 3/10; Bio-Rad, Hercules, CA]rsqb], 0.5% Triton x-100, and protease inhibitors) to six 100-mm culture dishes resurfaced with BCE-ECM, scraping off the ECM, and sonicating the resulting solution. The mixture was centrifuged, and the supernatant was transferred to a fresh tube. The pellet from this first solubilization step was further dissolved in the same lysis buffer with the addition of 1% NP-40, 1% Triton X-100, and 50 mM triethylammonium bicarbonate (TEAB). Proteins from the supernatant of the first solubilization step and from the solubilized pellet were subjected to analysis separately. One hundred micrograms of the proteins from each fraction were reduced by dithiothreitol (DTT) and alkylated with iodoacetamide followed by trypsin digestion overnight (trypsin to protein ratio was 1:20). The resulting peptides were separated by sequential ion exchange and reversed-phase liquid chromatography. The peptides were sequenced by tandem mass spectrometry techniques by using either matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF/TOF) or electrospray ionization (ESI) quadrupole time-of-flight (QTOF) mass spectrometry. In brief, the tryptic peptides were separated by strong cation-exchange chromatography (SCX) with a polysulfoethyl A column (4.6 × 200 mm, 5 μm diameter, 300 Å; Poly LC, Columbia, MD) on a perfusion chromatography system (BioCAD; AB Sciex, Foster City, CA). The peptides were eluted with a 40-minute linear gradient from 100% mobile phase A (10 mM KH
2PO
4 and 20% acetonitrile [ACN]) to 50% mobile phase B (600 mM KCl, 10 mM KH
2PO
4, and 20% ACN), followed by a 10-minute linear gradient from 50% to 100% B, at a flow rate of 1 mL/min. Fifteen fractions were collected, and the peptides were cleaned up on C
18 spin columns (Pierce, Rockford, IL). Desalted peptides were further separated by reversed-phase liquid chromatography (RPLC) with a capillary C
18 column (0.1 × 150 mm, 3 μm, 100 Å, C
18; PepMap; Dionex, Sunnyvale, CA) on an LC system (Ultimate 3000; Dionex) at a flow rate of 200 nL/min. A 70-minute gradient of solvent A (2% ACN, 0.1% trifluoroacetic acid [TFA for MALDI], or 0.1% formic acid [FA, for QTOF]) and solvent B (85% ACN, 0.1% TFA, for MALDI, or 0.1% FA, for QTOF) was used to elute the peptides from the C
18 column: 0 to 40 minutes, 2% to 22% B; at 65 minutes, to 40% B; and at 80 minutes, to 95% B. For MALDI MS analysis, the RPLC eluent was mixed with a MALDI matrix (5 mg/mL α-cyano-4-hydroxycinnamic acid [CHCA] in 60% ACN, 5 mM ammonium monobasic phosphate and internal calibrators, 50 fmol/μL each of GFP and ACTH 18-39) in a 1:3 ratio and spotted onto a MALDI plate in a 33 × 10 spot array. The peptides were analyzed on an MALDI-TOF/TOF mass analyzer (AB 4800; AB Sciex) in a plate-wide, data-dependent mode, to sequence the top 15 most abundant peptide ions in each MS spectrum. For LC-MS/MS analysis on QTOF, the RPLC eluent was directly introduced into a nano-ESI source on a QTOF tandem MS system (API-US; Waters Corp. Milford, MA), and the top three most abundant peptides were sequenced in a data-dependent mode. Protein identification was performed by searching the peak lists generated from MS/MS spectra against the bovine IPI database with a local MASCOT search engine (ver. 2.2) (Matrix Science Inc. Boston, MA). Oxidized methionine, carbamidomethyl modified cysteines were set as variable modifications in the search parameters. Proteins with at least one peptide ≥95% CI value were identified; overall the protein false-discovery rate was less than 1%. DAVID Bioinformatics Resources 6.7 was used to identify functional localization of proteins (
http://david.abcc.ncifcrf.gov/ provided in the public domain by the National Institute of Allergy and Infectious Diseases [NIAID], Bethesda, MD). Protein localization was cross referenced, and function was determined by GeneCards version 3 database (
http://www.genecards.org/ provided in the public domain by the Weizmann Institute of Science, Rehovot, Israel) or a protein knowledge database (
http://www.uniprot.org/ provided in the public domain by the European Molecular Biology Laboratory, Heidelberg, Germany).