biologically , the seed might bethe most critical stage of angiosperm development . indeed , the seed number per plant , their size and their ability to germinate are key components of plant fitness ( donohue et al . , . moreover , the seed structure helps plants to survive adverse environmental conditions but also helps to colonize new environments . concerning seed biology , our comprehension of fundamental biological processes such as dormancy or germination was greatly enhanced by the plant model arabidopsis thaliana used in combination with global  omics thus , modern functional genomics allow the characterization of cellular responses , gene network activation , and metabolic adaptation among a wide range of seed physiological states ( nambara and nonogaki , 2012 ) . these novel technologies represent powerful tools to accelerate basic and translational seed research . yet , to our knowledge , there are no publically accessible websites dedicated to the arabidopsis seed proteome . seed proteome web portal  to give free access to relevant data on the arabidopsis seed proteome . the spwp harbors a presentation of the founding laboratories , proteome data as well as detailed protocols and various links to bioinformatics resources or proteomic journals ( please see site map ) . the first main part of the spwp is focused on seed proteome data that can be accessed either from the protein maps or from the protein catalog ( figure 1a ) . as of today , information on the 475 protein spots identified during arabidopsis seed germination is available . in the protein map section , the user can retrieve a protein spot on a reference 2d gel obtained from arabidopsis seeds ( figure 1a ) . the protein spot can be selected directly on the 2d gel image to open a new page containing protein spot data ( figure 1b ) . on that new page , the  essential  table gives information on the protein spot class , spot number , protein name , description , gene number ( agi - id ) , and mascot peptide matches are given ( figure 1b ) . in the  data  and  sequences  table , the user can also find experimental proteomic facts such as the expected / observed molecular weight and isoelectric point together with the peptide sequences that allowed identification of the protein ( figure 1b ) . homepage ( a ) , 2d map of protein spots that increase during seed germination ( b ) and protocols for the detection of carbonylated proteins ( c ) and detection of de novo synthesized proteins ( d ) during seed germination . the second main part of the spwp offers a technical goldmine to scientists working on the seed proteome ( figure 1c ) . the user can find detailed protocols for a complete seed proteome experiment including seed germination , preparation of total protein extracts , 2d electrophoresis , gel staining , analysis of 2d gels , and protein identification by mass spectrometry are all explained in a detailed manner ( please also see rajjou et al . , 2011 ) . to our knowledge , there was no publically and freely available technical resource entirely dedicated to the study of the seed proteome . in addition , the spwp also gives some specific protocols to study seed sub - proteome such as the oxidized or de novo synthesized proteomes ( figure 1d ) . previous studies on the arabidopsis seed demonstrated the presence of a high number of long - lived mrna in the mature dry seed ( nakabayashi et al . , 2005 ) together with the absolute requirement for protein synthesis to germinate ( rajjou et al . , 2004 ) . during arabidopsis seed germination , we found a total of 475 protein spots corresponding unambiguously to 241 non - redundant proteins with a correspondence with a single agi i d . a total of 18 protein spots were matched to multiple agi - id ( table s1 in supplementary material ) . indeed , because of mrna processing , protein proteolysis and chemical protein modifications , one gene can produce many different protein isoforms resulting in a wide proteome diversity . each spot corresponds to a single protein isoform resulting from post - transcriptional or post - translational regulation of gene expression ( 1 mrna  =  x protein isoforms ) . a total of 250 protein spots showed an increasing abundance during germination sensu stricto ( 024  h ) or during radicle protrusion ( 2448  h ; figure 2 ) . otherwise , 143 protein spots displayed a decreasing abundance over the course of seed germination ( figure 2 ) . these results illustrate the major developmental switch that occurs during the germination phase in preparation for seedling establishment . indeed , while there are only three genes coding for 12s globulin seed storage protein in arabidopsis ( at1g03880 , at4g28250 , at5g44120 ) , a total of 104 protein spots corresponding to 12s globulin seed storage proteins can be retrieved on a 2d gel of seed proteins ( arc et al . , 2011 ) . spots corresponding to the precursor form of the globulin seed storage proteins can be processed by cleavage and transformed into their mature protein form ( gallardo et al . , 2001 ) . yet , at the seed proteome level , post - translational modifications by cleavage are not the most abundant modification as we found a good correlation between the theoretical and the observed protein molecular weight ( figure 3 ) . in contrast , we found a very poor correlation between the proteins theoretical and the observed isoelectric point ( figure 3 ; table s1 in supplementary material ) illustrating the major impact of post - translational modifications , e.g. , phosphorylation ( arc et al . , 2011 ) , glycosylation(vuylsteker et al . , 2000 ) , or oxidation ( job et al . , 2005 ) number of protein spots differentially accumulated during arabidopsis seed germination . for each time interval , the log2 ratio was calculated between 0 and 24  h as well as between 24 and 48  h. when the spot was not detected in one of the time point , a negligible spot abundance value was arbitrary assigned to calculate the log2ratio . ( a ) number of protein spots whose abundance is decreasing ( log2 ratio  < 1 ) between germination sensu stricto ( 024  h ) , radicle protrusion ( 2448  h ) or at both time intervals of seed imbibition . ( b ) number of protein spots whose abundance is increasing ( log2 ratio > 1 ) between germination sensu stricto ( 024  h ) , radicle protrusion ( 2448  h ) or at both time intervals of seed imbibition . theoretical and observed molecular weight and isoelectric points . the theoretical and observed molecular weights ( a ) as well as the theoretical and observed isoelectric point ( b ) from 457 protein spots with a unique agi - id are plotted . for both linear regressions , we investigated the specificity of the arabidopsis seed proteome by comparison with the leaf proteome data from the plant proteomics database ( sun et al . , 2009 ) and by the comparison with the entire arabidopsis proteome ( tair10 gene annotation data ) . first , we extracted the unambiguously identified non - redundant agi - id from the 475 protein spots of the seed proteome and classified them using the funcat catalog ( ruepp et al . , 2004 ) . we also classified the leaf proteome and the whole genome with the funcat catalog ( baerenfaller et al . , 2008 ) . after classification , we could observe that the  cell rescue , defense and virulence   energy , protein fate ,  and  storage protein  categories were over represented in the seed proteome as compared to the leaf proteome or entire proteome datasets ( figure 4 , table s2 in supplementary material ) . category contains catalase , superoxide dismutase and peroxiredoxin proteins that detoxify reactive oxygen species produced very early during germination ( bailly , 2004 ) . category encompasses many proteins from glycolysis ( e.g. , glyceraldehyde 3-phosphate dehydrogenase , pyruvate carboxylase ) as well as mitochondrial proteins from the tricarboxylic acid cycle ( e.g. , citrate synthase , succinyl - coa ligase ) or the glyoxylate cycle ( isocitrate lyase , malate synthase ) . thus , the seed proteome illustrates the high - energy demand in the seed upon metabolic resumption and it was recently shown that a majority of a 775 germination - specific gene subset was related to mitochondrial biogenesis ( narsai et al . , 2011 ) . the  protein fate  class of the seed proteome is composed of proteins involved in protein degradation ( e.g. , subunits of the 20s/26s proteasome ) , protein maturation ( e.g. , leucine aminopeptidase 1 ) or protein folding ( e.g. , heat shock proteins , peptidyl - prolyl cis - trans isomerase 1 , protein disulfide isomerase ) . finally , the  storage protein category is overrepresented in the seed proteome due to its developmental specificity and serves both as an amino acid storage pool as well as supplemental roles , since the alpha - subunits are preferentially oxidized during seed germination ( job et al . altogether , contrasting the funcat classification of the seed proteome , the leaf proteome and the entire arabidopsis proteome highlights the specificity of the seed proteome particularly concerning the energy demand and the correct protein folding necessary for seed germination . funcat annotation of the non - redundant proteins detected in the arabidopsis seed proteome . from the 475 different proteins of the seed proteome , we identified unambiguously 241 non - redundant proteins with a correspondence with a single agi - id . a total of 18 protein spots were matched to multiple agi - id i.e. grouped under an unique agi . the funcat catalog was used to annotate the seed proteome , the leaf proteome ( from baerenfaller et al . , 2008 ) and the entire arabidopsis proteome tair10 gene annotation data ; whole genome for comparisons . the most highly regulated genes during arabidopsis seed development tended to be expressed preferentially in seeds compared with other plant organs ( ruuska et al . , 2002 ) . moreover , a recent paper on both transcriptome and proteome during arabidopsis seed development showed that 56% of 319 protein / transcript pairs had concordant expression patterns ( hajduch et al . , 2010 ) . in the arabidopsis seed dry seed , more than 12000 stored mrna species were detected ( nakabayashi et al . , 2005 ) . this transcriptome is characterized both by a great number of stored mrna and by the rapid extensive changes occurring a few hours after imbibition ( nakabayashi et al . thus , due to the availability of the seed proteome , it was interesting to correlate the transcript and protein abundance variation during germination . indeed , we wondered if we could expect similar correlations between protein and transcript accumulation profiles during seed development and germination . the 475 protein spots were matched to their corresponding agi - id and , we obtained a non - redundant seed proteome of 241 proteins . then , the normalized abundance of each protein isoform corresponding to the same agi - id was summed . employing the transcriptome data from nakabayashi et al . ( 2005 ) , we analyzed the mrna accumulation corresponding to the 241 genes found in the seed non - redundant proteome . we obtained a probe signal for 218 genes and built a correlation between the transcript change and the protein change between 0 and 24  h after imbibition of non - dormant arabidopsis seeds ( figure 5 , table s3 in supplementary material ) . it was obvious that , during seed germination , there is no correlation between the transcript and the protein level ( r  =  0.02 ) . this is in accordance with the fact the long - lived stored mrna are present in the dry seed state and that protein synthesis is required for seed germination while transcription is not ( rajjou et al . , 2004 ; these observations suggest that there are no correlation between mrna and protein half - lives in arabidopsis seeds . therefore , both the transcriptome and the proteome analyses in the arabidopsis seed result in relevant information about the developmental switch occurring in the dry quiescent state to the metabolically active state . the transcript and protein abundance variation during seed germination are poorly correlated . from the 475 different proteins of the seed proteome , we identified 241 non - redundant proteins ( 241 agi ) . the transcript normalized abundance of 218 of these proteins was retrieved in the data from nakabayashi et al . for these 218 proteins , the log2 ratio between 0 and 24  h of seed germination was calculated for both transcript and protein . the corresponding values were then plotted and a correlation coefficient ( indicated on the graph ) was calculated from the linear regression . in a complementary approach , we took advantage of two independent studies designed to identify tissue - specific genes in arabidopsis by genome - wide transcriptome ( schmid et al . , 2005 ) or proteome ( baerenfaller et al . , 2008 ) approaches . to compare both transcriptome and proteome studies , we restricted our analysis to the  flower , leaves ,   root ,  and  seed  tissues as they were common in the two studies . altogether , 151 tissue - specific genes could be identified in these four tissues by transcriptomics while 469 could be identified by proteomics ( figure 6a , table s4 in supplementary material ) . surprisingly , we found that only 29 tissue - specific genes were commonly identified by the two approaches ( figure 6a ) . on closer examination , we found that 20 seed - specific genes were identified by both approaches out of a total of 190 seed - specific genes , i.e. , 57 seed - specific genes identified by transcriptomics plus 133 seed - specific genes identified by proteomics ( figure 6b , table s4 in supplementary material ) . this is in accordance with the poor correlation between rna and protein levels that we found for the 241 non - redundant proteins of the seed proteome ( figure 5 ) . finally , in a study on 319 protein / transcript pairs during arabidopsis seed filling , the observed correlation was equal to 56% ( hajduch et al . , 2010 ) . it suggests that the correlation between rna and protein levels is strongly reduced during seed germination , a key transition in a plants life . altogether , these analyses show that the seed transcriptome and proteome are not redundant and that each technique yields complementary biological information that reflects the importance of post - transcriptional as well as post - translational modifications in the seed . ( a ) number of distinct and common tissue - specific genes defined by transcriptome ( 151 genes , schmid et al . , 2005 ) or by proteome ( 469 genes , baerenfaller et al . , 2008 ) studies in the  leaf , root ,   flower ,  and  seed  samples . only samples commonly used in the two studies ( i.e. , flower , leaves , root , and seed ) ( b ) number of seed - specific genes identified by transcriptome ( schmid et al . , 2005 ) , proteome ( baerenfaller et al . , 2008 ) or both approaches . these data are complementary and non - redundant in comparison to seed transcriptome data in particular during arabidopsis seed germination . in addition , the great number of protein isoforms revealed by the 2d analysis highlights the seed proteome diversity currently underestimated due to the difficulty to detect low - abundant proteins . future developments of the spwp will first include proteins regulated by dormancy release in arabidopsis ( chibani et al . , 2006 ) as well as protein turnover ( l. rajjou , unpublished data ) . moreover , we will include proteomic studies on sugar beet ( beta vulgaris ) and rice ( oryza sativa ) germination . in addition , lc - ms / ms data on specific protein modifications such as carbonylation or phosphorylation during seed germination will be included to highlight the extent of post - translational modifications at this key development stage . finally , the recent progress in laser - assisted microdissection combined with shotgun proteomics by lc - ms / ms could be applied to describe the metabolic compartmentalization in the arabidopsis seed as it was done on other species ( gallardo et al . , 2007 ; the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest .
the seed proteome web portal ( spwp ; http://www.seed-proteome.com/ ) gives access to information both on quantitative seed proteomic data and on seed - related protocols . 
 firstly , the spwp provides access to the 475 different arabidopsis seed proteins annotated from two dimensional electrophoresis ( 2de ) maps . 
 quantitative data are available for each protein according to their accumulation profile during the germination process . 
 these proteins can be retrieved either in list format or directly on scanned 2de maps . 
 these proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination , up to radicle protrusion . during sensu stricto germination ( 24  h upon imbibition ) about 50% of the proteins display quantitative variations , exhibiting an increased abundance ( 35% ) or a decreasing abundance ( 15% ) . 
 moreover , during radicle protrusion ( 2448  h upon imbibition ) , 41% proteins display quantitative variations with an increased ( 23% ) or a decreasing abundance ( 18% ) . 
 in addition , an analysis of the seed proteome revealed the importance of protein post - translational modifications as demonstrated by the poor correlation ( r2  =  0.29 ) between the theoretical ( predicted from arabidopsis genome ) and the observed protein isoelectric points . secondly , the spwp is a relevant technical resource for protocols specifically dedicated to arabidopsis seed proteome studies . concerning 2d electrophoresis , the user can find efficient procedures for sample preparation , electrophoresis coupled with gel analysis , and protein identification by mass spectrometry , which we have routinely used during the last 12  years . 
 particular applications such as the detection of oxidized proteins or de novo synthesized proteins radiolabeled by [ 35s]-methionine are also given in great details . 
 future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination .