Abstract：
This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds and many sample types and experimental conditions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq, and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of proteins in the most recent B73 nuclear genome annotation. Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other B73 genome annotations will improve maize genome annotation. We also illustrate the high-confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, and K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical, and biological metadata. This new PeptideAtlas is integrated in MaizeGDB with a peptide track in JBrowse.
摘要：
本研究提供了玉米肽图谱资源（www。peptideatlas.org/builds/corem）来帮助解决有关玉米蛋白质组的问题。通过统一的处理和元数据注释管道，重新分析了从ProteomeXchange收集的玉米的公开原始串联质谱（MS/MS）数据。这些数据来自广泛的遗传背景和许多样品类型和实验条件。蛋白质搜索空间包括来自MaizeGDB的B73自交系的不同玉米基因组注释，UniProtKB,NCBIRefSeq,和W22自交系。搜索了4.45亿MS/MS光谱，其中120万个与37万个不同的肽相匹配。在最近的B73核基因组注释中,肽与66.2%的蛋白质匹配。此外，鉴定了最保守的质体和线粒体编码蛋白（NCBIRefSeq注释）。在其他B73基因组注释中鉴定的肽和蛋白质将改善玉米基因组注释。我们还说明了独特的W22蛋白的高置信度检测。N-末端乙酰化,磷酸化,泛素化，和三个赖氨酸酰化（K-乙酰基，K-丙二酰,和K-羟基异丁酰基）被鉴定出来，可以通过PeptideAtlas中的PTM查看器进行检查。所有匹配的MS/MS衍生肽数据与光谱，技术,和生物元数据。这种新的PeptideAtlas与JBrowse中的肽轨道集成在MaizeGDB中。
