Exhibit 99.2

UNAUDITED PRO FORMA COMBINED CONSOLIDATED FINANCIAL INFORMATION

On August 30, 2013, SciQuest, Inc. (“SciQuest”) acquired all of the outstanding capital stock of CombineNet, Inc. (“CombineNet”), a leading provider of advanced sourcing software. The acquisition of CombineNet expands SciQuest’s strategic sourcing footprint with an advanced, cloud-based tool that improves procurement decisions for spend categories that are typically beyond the capabilities of traditional eSourcing software. The purchase price consisted of approximately $26.6 million in cash and 819,970 shares of SciQuest’s common stock at a fair value of $17.1 million, of which $2.5 million in cash and 75,507 shares of common stock were deposited in escrow to satisfy potential indemnification claims. The purchase price is subject to an adjustment based on the closing amount of working capital of CombineNet. The acquisition was accounted for under the purchase method of accounting.

The unaudited pro forma combined consolidated balance sheet and statements of operations and accompanying notes referred to herein as the “Pro Forma Financial Statements” should be read in conjunction with:

The Pro Forma Financial Statements are presented for illustrative purposes only and are not indicative of either future results of operations or results that might have been achieved if the transaction had been consummated as of the date indicated. The Pro Forma Financial Statements are based upon currently available information and assumptions and estimates which SciQuest believes are reasonable. These assumptions and estimates, however, are subject to change. SciQuest’s management believes that all adjustments have been made that are necessary to fairly present the pro forma information.

SciQuest, Inc.

Unaudited Pro Forma Combined Consolidated Balance Sheet

As of June 30, 2013

(in thousands)

See accompanying notes to unaudited pro forma financial statements.

SciQuest, Inc.

Unaudited Pro Forma Combined Consolidated Statement of Operations

For the year ended December 31, 2012

(in thousands, except per share amounts)

See accompanying notes to unaudited pro forma financial statements.

SciQuest, Inc.

Unaudited Pro Forma Combined Consolidated Statement of Operations

For the six months ended June 30, 2013

(in thousands, except per share amounts)

See accompanying notes to unaudited pro forma financial statements.

SciQuest, Inc.

Notes to Unaudited Pro Forma Combined Consolidated Financial Statements

(in thousands)

1.  Basis of Pro Forma Presentation

The accompanying Pro Forma Financial Statements are based on the historical financial statements of SciQuest and CombineNet after giving effect to the acquisition of CombineNet by SciQuest using the purchase method of accounting and applying the assumptions and adjustments described in the accompanying notes.

The unaudited pro forma combined consolidated balance sheet as of June 30, 2013 gives effect to the transaction as if it had occurred on June 30, 2013. The unaudited pro forma combined consolidated statements of operations for the six months ended June 30, 2013 and the year ended December 31, 2012 give effect to the transaction as if it had occurred on January 1, 2012.

2.  Preliminary Purchase Price Allocation

The preliminary purchase consideration consisted of the following:

The purchase price was allocated on a preliminary basis to the tangible and identifiable intangible assets acquired and liabilities assumed based on their estimated fair values as of the acquisition date. The excess of the purchase price over the net tangible and identifiable intangible assets acquired was recorded as goodwill. The following summarizes the preliminary purchase price allocation:

3.  Pro Forma Adjustments

The following pro forma adjustments are included in the unaudited pro forma combined consolidated financial statements:

(A) To reflect the cash consideration paid of $26,575.

(B) To reclassify deferred commission costs from prepaid expenses to deferred project costs, to conform to SciQuest’s basis of presentation.

(C) To reflect the fair value adjustment related to CombineNet’s capitalized software development costs.

(D) To reflect the fair value of acquired goodwill based on net assets acquired and liabilities assumed as if the acquisition occurred on June 30, 2013. The difference between the amount recorded on a pro forma basis and the actual balance as of the effective date of the

acquisition is the result of changes in the assets and liabilities of CombineNet between June 30, 2013 and the closing date of August 30, 2013.

(E) To reflect the fair value of acquired definite-lived intangible assets consisting of customer relationships of $13,000, acquired technology of $4,100, trademarks of $300, and covenants not to compete of $100.

(F) To establish deferred tax assets and liabilities related to the acquisition. Long-term deferred tax assets and liabilities of SciQuest and CombineNet are presented on a net basis.

(G) To reflect the payoff of CombineNet’s line of credit of $500, and its current and long-term outstanding debt of $150 and $187, respectively, in connection with the acquisition.

(H) To reclassify CombineNet’s depreciation expense of $70 for the six months ended June 30, 2013 to cost of revenues of $17, research and development expense of $12, sales and marketing expense of $25, and general and administrative expense of $16, to conform to SciQuest’s basis of presentation.

(I) To reflect the fair value adjustment related to CombineNet’s deferred revenue balances.

(J) To remove amortization expense of $38 and $25 for the six months ended June 30, 2013 and the year ended December 31, 2012, respectively, related to CombineNet’s capitalized software development costs.

(K) To reflect the issuance of 819,970 shares of SciQuest’s common stock with a par value of $1 and a deemed value at issuance of $17,055.

(L) To eliminate the preferred stock, additional paid-in capital, accumulated other comprehensive loss, and accumulated deficit of CombineNet.

(M) To record amortization expense related to acquired definite-lived intangible assets.

(N) To reclassify CombineNet’s depreciation expense of $201 for the year ended December 31, 2012 to cost of revenues of $49, research and development expense of $37, sales and marketing expense of $73, and general and administrative expense of $42, to conform to SciQuest’s basis of presentation.

(O) To record acquisition costs of $431.

(P) To eliminate interest expense related to outstanding debt that was paid off in connection with the acquisition.

(Q) To record a reduction of $19 and $2,343 from revenues and other income, respectively, for the six months ended June 30, 2013, related to the estimated fair value adjustment of acquired deferred revenue.

(R) To record a reduction in revenues of $1,202 for the year ended December 31, 2012, related to the estimated fair value adjustment of acquired deferred revenue.

(S) To reflect the tax effect of the pro forma adjustments described above, utilizing SciQuest’s federal and state statutory rates.