Zimmerman Lisa J, Wernke Gregory R, Caprioli Richard M, Liebler Daniel C
Departments of Biochemistry and Pharmacology and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232, USA.
J Proteome Res. 2005 Sep-Oct;4(5):1672-80. doi: 10.1021/pr050138m.
The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to acquire spectral profiles has become a common approach to detect proteomic biomarkers of disease. MALDI-MS signals may represent both intact proteins as well as proteolysis products. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis can tentatively identify the corresponding proteins Here, we describe the application of a data analysis utility called FragMint, which combines MALDI-MS spectral data with LC-MS/MS based protein identifications to generate candidate protein fragments consistent with both types of data. This approach was used to identify protein fragments corresponding to spectral signals in MALDI-MS analyses of unfractionated human serum. The serum also was analyzed by one-dimensional SDS-PAGE and bands corresponding to the MALDI-MS signal masses were excised and subjected to in-gel digestion and LC-MS/MS analysis. Database searches mapped all of the identified peptides to abundant blood proteins larger than the observed MALDI-MS signals. FragMint identified fragments of these proteins that contained the MS/MS identified sequences and were consistent with the observed MALDI-MS signals. This approach should be generally applicable to identify protein species corresponding to MALDI-MS signals.
使用基质辅助激光解吸电离质谱法（MALDI-MS）获取光谱图谱已成为检测疾病蛋白质组学生物标志物的常用方法。MALDI-MS信号可能代表完整蛋白质以及蛋白水解产物。液相色谱-串联质谱（LC-MS/MS）分析可以初步鉴定相应的蛋白质。在此，我们描述了一种名为FragMint的数据分析工具的应用，该工具将MALDI-MS光谱数据与基于LC-MS/MS的蛋白质鉴定相结合，以生成与两种数据类型均一致的候选蛋白质片段。此方法用于鉴定在未分级人血清的MALDI-MS分析中与光谱信号相对应的蛋白质片段。血清还通过一维SDS-PAGE进行分析，切除与MALDI-MS信号质量相对应的条带，并进行胶内消化和LC-MS/MS分析。数据库搜索将所有鉴定出的肽段映射到比观察到的MALDI-MS信号大的丰富血液蛋白质上。FragMint鉴定出这些蛋白质的片段，这些片段包含MS/MS鉴定的序列并且与观察到的MALDI-MS信号一致。这种方法通常应适用于鉴定与MALDI-MS信号相对应的蛋白质种类。
