Improved short peptide identification using HILIC–MS/MS: Retention time prediction model based on the impact of amino acid position in the peptide sequence

Peptides: Production, bioactivity, functionality, and applications

“…This allows obtaining peptides subfractions with different hydrophobic behavior, but more than one RP-HPLC round will be required in order to obtain highly pure peptides in a sufficient amount (de Gobba et al, 2014a;Chi et al, 2015;Ruiz-Gim enez et al, 2012). Furthermore, hydrophilic interaction liquid chromatography (HILIC) has recently been suggested for an improved separation of homologous short peptides (Le Maux et al, 2015). Finally, these chromatographic techniques are coupled to mass spectrometry (MS), in particular to tandem MS (MS/MS), for peptide sequence determination.…”

“…Traditional identification approaches, which require the knowledge of the parent protein sequences, match tandem spectra with theoretical spectra derived from predicted peptides in a protein library (Espejo-Carpio et al, 2013;Gu and Wu, 2013;de Gobba et al, 2014b). Primary structure of proteins can be accessed from online databases such as UniProtKB/Swiss-Prot or NCBI and the identification process can be carried out by using database search engines (e.g., Mascot) (Dallas et al, 2015;Le-Maux et al, 2015). On the other hand, de novo sequencing approach does not require a protein library and deduces peptide amino acid sequence by calculating mass differences between fragments from the tandem mass spectra (Girgih et al, 2014;Garc ıa-Moreno et al, 2015).…”

Identification of short peptide sequences in the nanofiltration permeate of a bioactive whey protein hydrolysate

“…This is the case for chromatographic separation as peptide retention on a chromatographic matrix depends both on the sequence and the chromatographic conditions (Zou, Zhang, Hong, & Lu, 1992). The retention time of short peptides can be predicted using algorithm models based on properties such as peptide size and amino acid position within the peptide sequence (i.e., at the N-, the C-terminus or within the peptide sequence) (Krokhin, 2006;Le Maux, Nongonierma, & FitzGerald, 2015;Meek, 1980;Tripet et al, 2007). Furthermore, the combination of different separation modes such as hydrophilic interaction liquid chromatography (HILIC) and reverse-phase (RP) chromatography has been shown to further enhance the accuracy of short peptide identification (Harscoat-Schiavo et al, 2012).…”

“…Fisher Scientific (Waltham, MA, USA) as per Le Maux et al (2015). The whey protein substrate (88.3% (w/w) protein) was obtained from Carbery Food Ingredients (Ballineen,…”

Analysis of recombinant monoclonal antibodies in hydrophilic interaction chromatography: A generic method development approach

“…Such models regularly require several initial experimental runs, which make this approach time-consuming. Recently some quantitative structure-retention relationship (QSRR) based approaches were also reported for HILIC method development and retention prediction [3,[17][18][19]. In these studies, retention modeling was restricted to small molecules.…”