Brooks Automation, Inc. 3 rd Quarter Fiscal 2013 Financial Results Conference Call

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Brooks Automation, Inc. 3 rd Quarter Fiscal 2013 Financial Results Conference Call August 8, 2013

Safe Harbor Statement Safe Harbor Statement under the U.S. Private Securities Litigation Reform Act of 1995; certain matters in this presentation, including forecasts of future demand and future Company performance, are forward-looking statements that are subject to risks and uncertainties that could cause actual results to materially differ, either better or worse, from those projected. Further discussions s of risk factors are available a ab in the Company s most recent SEC filings including Form 10-K for the fiscal year ended September 30, 2012. The Company assumes no obligation to update the information in this presentation. Regulation G This presentation contains certain non-gaap measures which are provided to assist in an understanding of the Brooks business and its operational performance. These measures should always be considered in conjunction with the appropriate GAAP measure. Reconciliations of all non-gaap amounts to the relevant GAAP amount are provided in either an attachment to our third quarter financial results press release issued on August 8, 2013 or as an attachment to call slides used to accompany prepared comments made during our financial results conference call of the same date. Both documents are available on our website at www.brooks.com. 2

Significant Events in the June Quarter 1. Doubling of Life Science Systems order bookings to $18.5 million 2. Product revenues in Semi Front End declined as a result of exit from low margin businesses 3. Revenue growth for global service business and product sales into industrial and adjacent markets 4. Gross margin expansion in Life Sciences and Global Services segments 5. Reduced operating expenses from stock compensation accrual reversal 6. Abnormal (non cash) effective tax rate of 74% 5. $12.9 million cash flow from operations 3

Gross Margins Expand 150 bps $ millions Q2 FY13 Q3 FY13 Change Revenues $ 116.6 $ 118.1 $ 1.5 Gross profit * 37.4 39.7 2.3 Gross margin % 32.1% 33.6% 1.5% Research & development 12.0 12.1 ( 0.1) Selling, general & administrative 24.8 22.6 2.2 Operating Profit before special charges * $ 0.6 $ 5.0 $ 4.4 * Non GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure 4

Revenue and Operating Profits Waterfall $ millions Revenues Operating Profit before Special Charges* 2 nd nd Quarter Fiscal 2013 $ 116.6 $ 0.6 Brooks Product Solutions 1.2 0.1 Brooks Life Science Systems (0.3) 1.1 Brooks Global Services 0.6 1.1 Stock Compensation accrual reversal - 1.9 Other Operating Expenses - 0.2 3 rd Quarter Fiscal 2013 $ 118.1 $ 5.0 * Non GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure 5

GAAP and Adjusted Earnings $ millions Q2FY13 Q3FY13 Change Revenues $ 116.6 $ 118.1 $ 1.5 6 Operating profit (before special charges)* 0.6 5.0 4.4 Special charges* ( 1.6) ( 0.6) 10 1.0 Other items 0.4 0.6 0.2 Income taxes 0.1 ( 3.7) ( 3.8) Minorities & joint venture earnings 0.0 0.2 0.2 Net income (loss) attributable to Brooks $( 0.5) $ 1.5 $ 2.0 GAAP DEPS $ (0.01) $ 0.02 $ 0.03 Adjusted DEPS * $ 0.01 01 $ 0.03 03 $002 0.02 6 * Non GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

Fiscal 2013 Q3 Adjusted EBITDA $12.0 million Revenues Adj EBITDA R E V E N U E S 200 180 160 140 120 100 80 60 39% average 40 30 20 10 0-10 A D J E B I T D A * 40-20 * A non-gaap measure see SEC filings for reconciliations to GAAP measures 7 7

Fiscal 2013 Q3 Cash and Cash Flows $ millions Adjusted EBITDA * $ 12.0 Working Capital movements ( 3.3) Dividend from Joint Venture 4.6 Other operating items ( 0.4) Cash Flow from Operations 12.9 Capital expenditures ( 1.1) 1) Dividends ( 5.3) Other ( 1.3) Net Change in Cash and Marketable Securities 5.2 Cash and Marketable Securities at June 30, 2013 $ 150.7 8 * Non GAAP measure See www.brooks.com for reconciliation to the appropriate GAAP measure

June 2013 Condensed Balance Sheet CASH & MARKETABLE SECURITIES 151 $ Millions COMMENTS Accounts Receivable, net 86 Back-end loaded revenues Inventories 93 $4 million reduction in inventory Accounts Payable ( 31) Slower purchasing activity Deferred revenue ( 16) Upfront payments for Life Sciences Other current assets (liabilities), net ( 8) Net Working Capital 124 Net Fixed Assets 55 FY13 Capex. $5 - $6m Goodwill & other intangible assets 177 Other assets (liabilities), net 117 Shareholders Equity 624 Deferred Taxes / Joint Venture investment 9

Brooks Life Science Systems - Sequential Performance $ millions Q2FY13* Q3FY13 Revenues 9.1 8.8 Gross Profit 2.6 3.7 Comments on Sequential Trends Continued store revenue contraction ahead of rebound Software and device mix drive 42.2% gross margins Operating Expenses 6.3 6.2 Segment Operating Loss (3.7) (2.5) * Non GAAP measure excluding acquisition fair value adjustments. See appendix for a reconciliation to the appropriate GAAP measure 10

Brooks Product Solutions - Sequential Performance $ millions Q2FY13* Q3FY13 Revenues 85.4 86.6 Comments on Sequential Trends Industrial and adjacent market increases Gross Profit 28.0 28.1 Gross margin 32.4% Operating Expenses 24.2 23.0 Stock compensation accrual reversal Segment Operating Income 3.8 5.1 Operating margin 5.9% * Non GAAP measure excluding acquisition fair value adjustments. See appendix for a reconciliation to the appropriate GAAP measure 11

Brooks Global Services - Sequential Performance $ millions Q2FY13* Q3FY13 Comments on Sequential Trends Revenues 22.1 22.7 2.9% organic growth Gross Profit 6.8 7.9 Gross margin 34.8% including inventory recoveries Operating Expenses 4.6 3.9 Crossing integration Segment Operating Income 2.2 4.0 Operating margin 17.5% * Non GAAP measure excluding acquisition fair value adjustments. See appendix for a reconciliation to the appropriate GAAP measure 12

Revenue Trends Excluding Contract Manufacturing Business 150 $ millions Mid Point of guidance 120 90 60 30 0 Semi FE Products Industrial Adjacent Service Life Sciences 13 2013 Brooks Automation, 13Inc. Proprietary Information

Significant Events since June 30 1. On July 31, entered into a definitive agreement to sell an owned building on the Chelmsford campus for $11.4 million The Company expects to recognize a gain of approximately $1 million on closing this transaction later in the September quarter 2. On August 1, closed the acquisition of the business and assets of Matrical, Inc. for total cash consideration of $10.3 million Matrical, based in Spokane, WA,will be integrated into our Brooks Life Science ce Systems s business Matrical reported revenues of approximately $9 million in their latest fiscal year financials 14

Revenue, EBITDA & Earnings Guidance Q3FY13 Q4FY13 Comments on Sequential Trends Revenues ($ millions) $ 118.1 $113.0 - $118.0 Life Sciences revenue growth Industrial and Service revenue declines Adjusted EBITDA* $ 12.0 $ 10.0 - $13.0 Drives favorable cash flow Adjusted Diluted Earnings Per Share* $ 0.03 $0.02 $0.05 Effective tax rate of <3% as compared to 74% in Q3 FY13 GAAP Diluted Earnings Per Share $ 0.02 $0.03- $0.06 One-time gain from building sale and Matrical purchase accounting * Non GAAP measure. See www.brooks.com for reconciliation of historical measure to GAAP measure 15 15

Brooks Automation, Inc. 3 rd Quarter Fiscal 2013 Financial Results Conference Call August 8, 2013 16

GAAP to Non-GAAP Reconciliation Consolidated P&L GAAP non-gaap GAAP non-gaap in millions Q2 FY13 Adjust Q2 FY13 Q3 FY13 Adjust Q3 FY13 Revenues $ 116.6 $ - $ 116.6 $ 118.1 $ - $ 118.1 Cost of revenues 80.0 (0.8) 79.2 78.4-78.4 Gross profit 36.6 0.8 37.4 39.7-39.7 Operating expense: 32.1% 33.6% Research & development 12.0-12.0 12.1-12.1 Selling, general & administrative 24.8-24.8 22.6-22.6 Restructuring 0.8 (0.8) - 0.6 (0.6) - Pension settlement - - - - - - 37.6 (0.8) 36.8 35.3 (0.6) 34.7 Operating profit (loss) (1.0) 1.6 0.6 4.4 0.6 5.0 Interest income, net 0.3-0.3 0.2-0.2 Other, net 0.1-0.1 0.4-0.4 Income before taxes, joint ventures and minority interest (0.6) 1.6 1.0 5.0 0.6 5.6 Income tax provision (0.1) 0.5 0.4 3.7 0.2 3.9 Net income before joint ventures and minority interest (0.5) 1.1 0.6 1.3 0.4 1.7 Joint venture income (losses) (0.0) - (0.0) 0.2-0.2 Net income (0.5) 1.1 0.6 1.5 0.4 1.9 Net (income) loss attributable to minority interests (0.0) - (0.0) (0.0) - (0.0) Net income (loss) attributable to Brooks $ (0.5) $ 1.1 $ 0.6 $ 1.5 $ 0.4 $ 1.9 Basic earnings per share attributable to Brooks $ (0.01) $ 0.02 $ 0.01 $ 0.02 $ 0.01 $ 0.03 Diluted earnings per share attributable to Brooks $ (0.01) $ 0.02 $ 0.01 $ 0.02 $ 0.01 $ 0.03 Basic shares for EPS 65,889 65,889 65,889 66,041 66,041 66,041 Diluted shares for EPS 65,889 66,509 66,509 66,687 66,687 66,687 Adjustments Cost of revenues: Purchase accounting impact on inventory acquired $ (0.8) $ - Operating expense: Restructuring $ (0.8) $ (0.6) Merger costs 0.0 (0.0) Pension settlement - - $ (0.8) $ (0.6) Income tax provision Tax impact from Non-GAAP adjustments $ 0.4 $ 0.2 17

GAAP to Non-GAAP Reconciliation Segments Q2 Brooks Product Solutions Brooks Global Services Brooks Life Science Systems GAAP non-gaap GAAP non-gaap GAAP non-gaap in millions Q2 FY13 Adjust Q2 FY13 Q2 FY13 Adjust Q2 FY13 Q2 FY13 Adjust Q2 FY13 Revenues $ 85.4 $ - $ 85.4 $ 22.1 $ - $ 22.1 $ 9.1 $ - $ 9.1 Cost of revenues 57.7 (0.3) 57.4 15.6 (0.3) 15.3 6.7 (0.2) 6.5 Gross profit 27.7 0.3 28.0 6.5 0.3 6.8 2.4 0.2 2.6 Operating expenses 24.2-24.2 4.6-4.6 6.3-6.3 Operating profit (loss) $ 3.5 $ 0.3 $ 3.8 $ 1.9 $ 0.3 $ 2.2 $ (3.9) $ 0.2 $ (3.7) Adjustments Cost of revenues: Purchase accounting impact on inventory acquired $ (0.3) $ (0.3) $ (0.2) 18 2012 Brooks Automation, Inc. Proprietary Information

GAAP to Non-GAAP Reconciliation Segments Q3 Brooks Product Solutions Brooks Global Services Brooks Life Science Systems GAAP non-gaap GAAP non-gaap GAAP non-gaap in millions Q3 FY13 Adjust Q3 FY13 Q3 FY13 Adjust Q3 FY13 Q3 FY13 Adjust Q3 FY13 Revenues $ 86.6 $ - $ 86.6 $ 22.7 $ - $ 22.7 $ 8.8 $ - $ 8.8 Cost of revenues 58.5-58.5 14.8-14.8 5.1-5.1 Gross profit 28.1-28.1 7.9-7.9 3.7-3.7 Operating expenses 23.0-23.0 3.9-3.9 6.4-6.4 Operating profit (loss) $ 5.1 $ - $ 5.1 $ 4.0 $ - $ 4.0 $ (2.7) $ - $ (2.7) Adjustments Cost of revenues: Purchase accounting impact on inventory acquired $ - $ - $ - 19 2012 Brooks Automation, Inc. Proprietary Information