JNJ-42756493 site proteins with local FDR < 1 were accepted as detected (Additional files 10, 11, 12, 13, 14, 15, 16, 17, and 18).Lu et al. BMC Plant Biology (2016) 16:Page 15 ofProteomics data analysisWe combined proteins detected in ask1 samples into the ask1 proteome, and combined proteins detected in Ler into the Ler proteome. We first compared our ask1 and Ler proteomes to find proteins that are only detected in ask1 samples. We also obtained previously published proteomics data of wild-type Arabidopsis thaliana floral buds [46, 47] and combined them into a "previous WT" proteome containing 5461 non-redundant proteins (FDR < 1 ). Comparison of our Ler and ask1 proteomes with the previous WT proteome resulted in the finding of additional floral proteins in our data. We combined our Ler floral bud proteome with the wcs.1183 previous WT proteome [46, 47] to a “Pooled WT” proteome consisting srep43317 of 5977 non-redundant proteins. Comparison of our ask1 proteome with the Pooled WT proteome led to the identification of proteins that are considered as “ask1only” proteins. Since each sample was analyzed by MudPIT individually without labeling and multiplexing, the abundance of each protein cannot be directly compared across different samples. Instead, the relative abundance of each protein in a sample was normalized using the spectral counting method as previously described [46, 48?1, 87]. The following formula is used to calculate the spectral counting values which represent the normalized relative abundance of proteins:hAbundance of protein Kwere compared. Proteins whose average spectral counting value in ask1 samples is at least 1.5-fold of that in Ler samples were considered as “ask1-higher” proteins.Availability of supporting dataThe data sets supporting the results of this article are included within the article and its additional file. The raw microarray datasets were deposited in the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) with the accession number GSE42841.Additional filesAdditional file 1: Genes up-regulated in the ask1 mutant microarray compared with Ler. Additional file 2: Genes down-regulated in the ask1 mutant microarray compared with Ler. Additional file 3: Proteins detected in individual proteomics samples with FDR < 1 . Additional file 4: Three membrane protein categories are well represented in the detected Ler and ask1 proteins (FDR < 1 ). Additional file 5: ask1-only proteins with microarray values. Additional file 6: ask1-higher proteins with spectral counting and microarray values. Additional file 7: ask1-lower proteins with spectral counting and microarray values. Additional file 8: The ask1 mutant has reduced female fertility. Additional file 9: Normalized microarray data of three biological replicates of ask1 and four biological replicates of Ler floral buds. Additional file 10: Mass spectrometry data of ask1_1 sample exported as .zip file. Additional file 11: Mass spectrometry data of ask1_2 sample exported as .zip file. Additional file 12: Mass spectrometry data of ask1_3 sample exported as .zip file. Additional file 13: Mass spectrometry data of ask1_4 sample exported as .zip file. Additional file 14: Mass spectrometry data of ask1_5 sample exported as .zip file. Additional file 15: Mass spectrometry data of Ler_1 sample exported as .zip file. Additional file 16: Mass spectrometry data of Ler_2 sample exported as .zip file. Additional file 17: Mass spectrometry data of Ler_3 sample expor.