Proteome公司Scaffold2.1軟件現支持安捷倫SpectrumMill搜索平臺

2008年8月7日安捷倫科技  分析測試百科 譯
SANTA CLARA, Calif., and PORTLAND, Ore.,

安捷倫科技和蛋白質組軟件公司（Proteome Software）今天宣布，Proteome公司的Scaffold 2.1版本軟件，現在可以處理從安捷倫的Spectrum Mill 蛋白數據庫搜索引擎中搜索的結果。

Scaffold可對串聯質譜數據進行統計學認證，從多個搜索引擎中合并結果，并用圖像顯示在生物學相關的形態中的鑒定結果。Spectrum Mill 可對MS和MS/MS數據進行高通量的蛋白質數據庫檢索。 

研究者可以把Spectrum Mill數據文件裝載（load）到Scaffold中，然后把Spectrum Mill 的結果和各種搜索引擎結果比較，比如：Mascot，SEQUEST，Phenyx，OMSSA 和 X!Tandem。

“通過支持Spectrum Mill搜索引擎，Scaffold為它的集成庫增加了另一個優秀的工具，使研究者們可以更容易地合并、比較、分享MS/MS檢索結果。” Proteome公司的科學家Christopher Mason說。

“合并的搜索引擎數據，比任何單一的搜索引擎產生好得多的結果。”安捷倫實驗室的研究者Alex Apffel博士說。“用戶可以'拯救'那些可能會被拒絕的譜圖；并為結果的評價提供了一個客觀的統計基礎。”

安捷倫實驗室，該公司的中央研究機構同Proteome軟件公司合作，集成了Spectrum Mill 和Scaffold，幫助研究者獲得更高質量的數據。用于MassHunter工作站的Spectrum Mill 新版本，有幾項獨特的性能：

• 接受多數質譜儀器的數據；
• 是少數幾個可以利用高質量精度MS和MS/MS譜圖的軟件之一，可以提高搜索結果的特異性和置信度
• 可以方便地鑒定未知的蛋白修飾；
• 提供優良的可視化工具，幫助自動和手動地驗證、檢查搜索結果，并顯示差異的表達譜

若想下載Scaffold 2.1，請訪問：www.proteomesoftware.com.

關于安捷倫的Spectrum Mill

MassHunter工作站上使用的Spectrum Mill，即使對于非常復雜的查詢，反饋也很快速（~200 毫秒/張譜）。它通過快速的數據庫搜索，獨特的算法，智能并行和迭代搜索過程，快速地鑒定蛋白質和多肽。Spectrum Mill有多種操作模式：在鑒定模式下找到未修飾的肽段；在可變修飾或同源模式下可尋找翻譯后修飾、變異或化學修飾。對于數據庫中找不到的肽段，也可以進行從頭（de novo）的譜圖解析。Spectrum Mil可在無需同位素標記的情況下，鑒定兩個數量級（或更高）的相對豐度差異；同時也支持所有的標記技術。

關于Proteome公司的軟件

Scaffold 2.1是工業標準級的MS/MS后分析工具，對于串聯質譜實驗鑒定的蛋白，它給出一種完整的、實驗性的展現。Scaffold幫助蛋白質組學研究人員驗證，可視化，并分享他們的數據。更多關于Scaffold 2.1的信息，請訪問：www.proteomesoftware.com

參考引文原文：

Agilent Technologies' Spectrum Mill Searches Now Supported in Proteome Software's Scaffold 2.1

[August 7, 2008 Agilent Technologies]
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SANTA CLARA, Calif., and PORTLAND, Ore., Aug. 6, 2008

Agilent Technologies and Proteome Software today announced that Proteome's Scaffold 2.1 software now supports the processing of search results from Agilent's Spectrum Mill protein database search engine.

Scaffold statistically validates peptides and proteins from tandem mass spectrometry data, combines results from multiple search engines and graphically displays identifications in biologically relevant formats. Spectrum Mill performs high-throughput protein database searches of MS and MS/MS data.

Researchers who load Spectrum Mill data files into Scaffold can now compare Spectrum Mill results with those of Mascot, SEQUEST, Phenyx, OMSSA and X!Tandem search engines.

"By supporting the Spectrum Mill search engine, Scaffold has added another excellent tool to its arsenal, making it even easier for researchers to combine, compare, and share MS/MS search results," noted Christopher Mason, staff scientist at Proteome Software.

"Combining search engine data yields a far better result than would be obtained with any one search engine," said Dr. Alex Apffel, Agilent Laboratories researcher. "Users can 'rescue' spectra that would otherwise be rejected and provide an objective statistical basis for evaluation of results."

Agilent Laboratories, the company's central research organization, collaborated with Proteome Software to help researchers achieve higher-quality data through the integration of Spectrum Mill and Scaffold. The new version of Spectrum Mill for MassHunter Workstation offers a number of unique capabilities:

Accepts data from most mass spectrometric instruments;
Is one of a few programs that exploit high mass accuracy data in MS and MS/MS spectra for improved specificity and confidence in search results;
Allows easy identification of unexpected protein modifications; and
Offers superior visualization tools to aid in automatic and manual validation, inspection of search results and display of differential expression.
To download Scaffold 2.1, please visit www.proteomesoftware.com.

About Agilent's Spectrum Mill

Spectrum Mill for MassHunter Workstation from Agilent Technologies provides rapid (~200 msec/spectrum) turnaround even for complex queries. It quickly identifies proteins and peptides via fast database searches, unique algorithms, intelligent parallelization and iterative search processes. Spectrum Mill can operate in identity mode to find unmodified peptides, or in variable modifications or homology mode to look for post-translational modifications, mutations, and chemical modifications. It also offers de novo spectral interpretation for peptides not found in any database. Spectrum Mill software can identify relative abundance differences of twofold or greater without complicated isotope labeling, but also supports all common labeling techniques.

About Proteome Software

Scaffold 2.1 Software is the industry-standard MS/MS meta-analysis tool that displays a complete, experiment-wide view of the proteins identified in a tandem mass spectrometry experiment. Scaffold helps proteomics researchers validate, visualize, and share their data. More information about Scaffold 2.1 is available on the web at www.proteomesoftware.com.