Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents
Continued development of a new sequence−specific algorithm for peptide retention prediction in RP HPLC is reported. Our discovery of the large effect on the apparent hydrophobicity of N-terminal amino acids produced by the ion-pairing retention mechanism has led to the development of sequence-specif...
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| Veröffentlicht in: | Analytical chemistry (Washington) 2006-11, Vol.78 (22), p.7785-7795 |
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| creator | Krokhin, Oleg V |
| description | Continued development of a new sequence−specific algorithm for peptide retention prediction in RP HPLC is reported. Our discovery of the large effect on the apparent hydrophobicity of N-terminal amino acids produced by the ion-pairing retention mechanism has led to the development of sequence-specific retention calculator (SSRCalc) algorithms. These were optimized for a set of ∼2000 tryptic peptides confidently identified by off-line microHPLC−MALDI MS (MS/MS) (300-Å pore size C18 sorbent, linear water/acetonitrile gradient, and trifluoroacetic acid as ion-pairing modifier). The latest version of the algorithm takes into account amino acid composition, position of the amino acid residues (N- and C-terminal), peptide length, overall hydrophobicity, pI, nearest-neighbor effect of charged side chains (K, R, H), and propensity to form helical structures. A correlation with R 2∼0.98 was obtained for the 2000-peptide optimization set. A flexible structure for the SSRC programming code allows easy adaptation to different chromatographic conditions. This was demonstrated by adapting the algorithm (∼0.98 R 2 value) for a set of ∼2500 peptides separated on a 100-Å pore size C18 column. The SSRCalc algorithm has also been extensively tested for a number of real samples, providing solid support for protein identification and characterization; correlations in the range of 0.95−0.97 R 2 value have normally been observed. |
| doi_str_mv | 10.1021/ac060777w |
| format | Article |
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The latest version of the algorithm takes into account amino acid composition, position of the amino acid residues (N- and C-terminal), peptide length, overall hydrophobicity, pI, nearest-neighbor effect of charged side chains (K, R, H), and propensity to form helical structures. A correlation with R 2∼0.98 was obtained for the 2000-peptide optimization set. A flexible structure for the SSRC programming code allows easy adaptation to different chromatographic conditions. This was demonstrated by adapting the algorithm (∼0.98 R 2 value) for a set of ∼2500 peptides separated on a 100-Å pore size C18 column. 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Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>Continued development of a new sequence−specific algorithm for peptide retention prediction in RP HPLC is reported. Our discovery of the large effect on the apparent hydrophobicity of N-terminal amino acids produced by the ion-pairing retention mechanism has led to the development of sequence-specific retention calculator (SSRCalc) algorithms. These were optimized for a set of ∼2000 tryptic peptides confidently identified by off-line microHPLC−MALDI MS (MS/MS) (300-Å pore size C18 sorbent, linear water/acetonitrile gradient, and trifluoroacetic acid as ion-pairing modifier). The latest version of the algorithm takes into account amino acid composition, position of the amino acid residues (N- and C-terminal), peptide length, overall hydrophobicity, pI, nearest-neighbor effect of charged side chains (K, R, H), and propensity to form helical structures. A correlation with R 2∼0.98 was obtained for the 2000-peptide optimization set. A flexible structure for the SSRC programming code allows easy adaptation to different chromatographic conditions. This was demonstrated by adapting the algorithm (∼0.98 R 2 value) for a set of ∼2500 peptides separated on a 100-Å pore size C18 column. 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Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents</title><author>Krokhin, Oleg V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a323t-102a4af409fbdf1f0eb5fce8f259554f05b00fca4886fdc01b710eeb114076253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Acetonitriles - chemistry</topic><topic>Algorithms</topic><topic>Amino acids</topic><topic>Amino Acids - chemistry</topic><topic>Amino Acids - isolation & purification</topic><topic>Analytical chemistry</topic><topic>Chemistry</topic><topic>Chromatographic methods and physical methods associated with chromatography</topic><topic>Chromatography, High Pressure Liquid - methods</topic><topic>Exact sciences and technology</topic><topic>Hydrophobic and Hydrophilic Interactions</topic><topic>Ions</topic><topic>Molecular Weight</topic><topic>Other chromatographic methods</topic><topic>Particle Size</topic><topic>Peptides</topic><topic>Peptides - chemistry</topic><topic>Peptides - isolation & purification</topic><topic>Pore size</topic><topic>Porosity</topic><topic>Protein Structure, Secondary</topic><topic>Silanes - chemistry</topic><topic>Spectrometric and optical methods</topic><topic>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</topic><topic>Trifluoroacetic Acid - chemistry</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Krokhin, Oleg V</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Analytical chemistry (Washington)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Krokhin, Oleg V</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents</atitle><jtitle>Analytical chemistry (Washington)</jtitle><addtitle>Anal. Chem</addtitle><date>2006-11-15</date><risdate>2006</risdate><volume>78</volume><issue>22</issue><spage>7785</spage><epage>7795</epage><pages>7785-7795</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><coden>ANCHAM</coden><abstract>Continued development of a new sequence−specific algorithm for peptide retention prediction in RP HPLC is reported. Our discovery of the large effect on the apparent hydrophobicity of N-terminal amino acids produced by the ion-pairing retention mechanism has led to the development of sequence-specific retention calculator (SSRCalc) algorithms. These were optimized for a set of ∼2000 tryptic peptides confidently identified by off-line microHPLC−MALDI MS (MS/MS) (300-Å pore size C18 sorbent, linear water/acetonitrile gradient, and trifluoroacetic acid as ion-pairing modifier). The latest version of the algorithm takes into account amino acid composition, position of the amino acid residues (N- and C-terminal), peptide length, overall hydrophobicity, pI, nearest-neighbor effect of charged side chains (K, R, H), and propensity to form helical structures. A correlation with R 2∼0.98 was obtained for the 2000-peptide optimization set. A flexible structure for the SSRC programming code allows easy adaptation to different chromatographic conditions. This was demonstrated by adapting the algorithm (∼0.98 R 2 value) for a set of ∼2500 peptides separated on a 100-Å pore size C18 column. The SSRCalc algorithm has also been extensively tested for a number of real samples, providing solid support for protein identification and characterization; correlations in the range of 0.95−0.97 R 2 value have normally been observed.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>17105172</pmid><doi>10.1021/ac060777w</doi><tpages>11</tpages></addata></record> |
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| ispartof | Analytical chemistry (Washington), 2006-11, Vol.78 (22), p.7785-7795 |
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| source | MEDLINE; American Chemical Society Journals |
| subjects | Acetonitriles - chemistry Algorithms Amino acids Amino Acids - chemistry Amino Acids - isolation & purification Analytical chemistry Chemistry Chromatographic methods and physical methods associated with chromatography Chromatography, High Pressure Liquid - methods Exact sciences and technology Hydrophobic and Hydrophilic Interactions Ions Molecular Weight Other chromatographic methods Particle Size Peptides Peptides - chemistry Peptides - isolation & purification Pore size Porosity Protein Structure, Secondary Silanes - chemistry Spectrometric and optical methods Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods Trifluoroacetic Acid - chemistry Water - chemistry |
| title | Sequence-Specific Retention Calculator. Algorithm for Peptide Retention Prediction in Ion-Pair RP-HPLC: Application to 300- and 100-Å Pore Size C18 Sorbents |
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