Searching for specific motifs in affinity capture in proteome analysis

In analysing the red blood cell cytoplasmic proteome, in search for low abundance proteins, 15 amino acid (AA; Arg, Asn, Asp, Gln, Gly, His, Ile, Lys, Phe, Pro, Ser, Thr, Trp, Tyr, and Val) probes, used individually, captured a total of 787 unique gene products. Of those, 76 were found to be the common catch of all AA probes, 497 were captured by more than one (but not all) probe, and 214 were captured by only one probe. By using the InterPro database, for 151 of the 214 IPIs associated with proteins captured by a single amino acid, we have found 265 annotations of motifs (231 protein domains, 3 binding sites, 3 active sites, 13 conserved sites, and 15 repeats). Among these 151 proteins annotated, there are 75 domains, 2 active sites, 5 conserved sites, and 3 repeats (a total of 85 motifs) that are at all effects amino acid strictly specific. As a result of these findings, these 85 amino acid specific motifs singled out 40 (18.69%) of the total list of 214 proteins representing the total capture of the 15 AAs here reported. If one considers that only for 151 (70.56%) of the 214 proteins data about interacting motifs could be collected, the percentage of proteins for which the 85 amino acid strictly specific motifs have been found increases to the even more relevant value of 26.49%. The identified motifs can partially explain the exclusive protein capture of the 15 amino acid probes. The unique general and specific capturing ability of two of these AA probes, Phe and Arg, is evaluated, discussed and put in perspective.