SCAPE:  A New Tool for the Selective CApture of PEptides in Protein Identification

Abstract

A method for the selective capture and analysis of peptides containing neither histidine nor arginine is evaluated. It is based on the reversible modification of alpha- and epsilon-amino groups of peptides and the relatively easy separation of charged and noncharged peptides by cation exchange chromatography. The simplicity of the method and the results obtained in silico and with standard proteins, anticipate the utility of the SCAPE approach for proteome analyses.

In silico analysis of accurate proteomics, complemented by selective isolation of peptides

“…There are methodologies devised for selectively isolating sets of peptides that share a common sequence motif, such as ICAT [21], COFRADIC [22] and SCAPE [24]. These technologies simplify considerably the complexity of the starting peptide mixture, and are designed to ease the analysis of complex samples in proteomic studies.…”

“…Also, we evaluated tryptic peptides with reversibly blocked primary amine groups separated by cation exchange chromatography according to their number of positive charges (manuscript in preparation). These peptide sets are: (4) neutral peptides (previously denominated as nHnR [24] and here denominated as RH0, where #R+ #H =0): (5) peptides that contains either one arginine or one histidine (RH1, where #R+ #H= 1): and (6) multiply-charged peptides (RH2, where the #R+ #H> 1) [25]. Fig.…”

“…The development of methods that simply attempt to reduce sample complexity by selectively obtaining representative peptide subsets has emerged as an alternative approach for the analysis of complex samples. [20][21][22][23][24] The selective peptide isolation methods developed by our group, are based on the modification of abundant functional groups such as the α-and ε-amino groups of tryptic fragments in combination with well-established chromatographic techniques such as cation exchange [24][25][26] or affinity chromatography [25,26]. This, while still guaranteeing the isolation of a reduced set of peptides (3-4 per protein), increases the likelihood that all proteins from the original sample will be represented in the isolated subset, thus increasing proteome coverage.…”

“…This, while still guaranteeing the isolation of a reduced set of peptides (3-4 per protein), increases the likelihood that all proteins from the original sample will be represented in the isolated subset, thus increasing proteome coverage. Three methods have been developed to isolate, with high selectivity, different peptides sharing specific sequence features: (1) peptides containing neither arginine nor histidine residues (RH0 peptides) [24,26]; (2) multiply-charged peptides where the number of arginine and/or histidine residues is higher than one (R+H>1, RH2 peptides) [25]; (3) tryptic peptides devoid of Lys residues, derived from cleavages at arginine residues (RH1 peptides) [26].…”

Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches

“…Our group has reported several selective isolation methods based on chemical modification of peptide primary amino groups [8][9][10][11][12]. In this work, an integrating approach of these methods into a new separation scheme was developed.…”