Mizero, B.; Yeung, D.; Spicer, V.; Krokhin, O. V., Peptide retention time prediction for peptides with post-translational modifications: N-terminal (alpha-amine) and lysine (epsilon-amine) acetylation. J Chromatogr A 2021, 1657, 462584.
Peptide retention time prediction for peptides with post-translational modifications: N-terminal (α-amine) and lysine (ε-amine) acetylation - PubMed
Development of a peptide retention prediction model in reversed-phase chromatography is reported for acetylated peptides - both N-terminal (α-) and side chain of Lys (ε-amine) residues. Large-scale proteomic 2D LC-MS analyses of acetylated/non-acetylated tryptic digest of whole human cell lysate hav ...
pubmed.ncbi.nlm.nih.gov
Chang, C. H.; Yeung, D.; Spicer, V.; Ogata, K.; Krokhin, O.; Ishihama, Y., Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res 2021. doi: 10.1021/acs.jproteome.1c00185
Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry
The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values.
pubs.acs.org
Villacres, C.; Spicer, V.; Krokhin, O. V., Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction. J Proteome Res 2021,
20 (3), 1571-1581.
Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction
The chromatographic behavior of peptides carrying citrulline and homocitrulline residues in proteomic two-dimensional (2D) liquid chromatography-mass spectrometry (LC-MS) experiments has been investigated. The primary goal of this study was to determine the chromatographic conditions that allow differentiating between arginine citrullination and deamidation of asparagine based on retention data, improving the confidence of MS-based identifications.
pubs.acs.org
Yeung, D.; Mizero, B.; Gussakovsky, D.; Klaassen, N.; Lao, Y.; Spicer, V.; Krokhin, O. V., Separation Orthogonality in Liquid Chromatography-Mass Spectrometry for Proteomic Applications: Comparison of 16 Different Two-Dimensional Combinations. Anal Chem 2020, 92 (5), 3904-3912.
Separation Orthogonality in Liquid Chromatography-Mass Spectrometry for Proteomic Applications: Comparison of 16 Different Two-Dimensional Combinations
Peptide separation orthogonality for 16 different 2D LC-ESI MS systems has been evaluated. To compare and contrast the behavior of the first dimension columns, a large proteomic retention data set of ∼30 000 tryptic peptides was collected for each 2D pairing.
pubs.acs.org
Gussakovsky, D.; Anderson, G.; Spicer, V.; Krokhin, O. V., Peptide separation selectivity in proteomics LC-MS experiments: Comparison of formic and mixed formic/ heptafluorobutyric acids ion-pairing modifiers. J Sep Sci 2020, 43 (20), 3830-3839.
https://pubmed.ncbi.nlm.nih.gov/32818315/
1 Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada. 2 Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada. 3 Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada. 1 Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada. 2 Manitoba Centre for Proteomics and Systems Biology, Winnipeg, Manitoba, Canada.
pubmed.ncbi.nlm.nih.gov
Yeung, D.; Klaassen, N.; Mizero, B.; Spicer, V.; Krokhin, O. V., Peptide retention time prediction in hydrophilic interaction liquid chromatography: Zwitter-ionic sulfoalkylbetaine and phosphorylcholine stationary phases. J Chromatogr A 2020, 460909.
Peptide retention time prediction in hydrophilic interaction liquid chromatography: Zwitter-ionic sulfoalkylbetaine and phosphorylcholine stationary phases - PubMed
Peptide retention time prediction models have been developed for zwitter-ionic ZIC-HILIC and ZIC-cHILIC stationary phases (pH 4.5 eluents) using proteomics-derived retention datasets of ~30 thousand tryptic peptides each. Overall, hydrophilicity of these stationary phases was found to be similar to ...
pubmed.ncbi.nlm.nih.gov
Klaassen, N.; Spicer, V.; Krokhin, O. V., Universal retention standard for peptide separations using various modes of high-performance liquid chromatography. J Chromatogr A 2019, 1588, 163-168.
Universal retention standard for peptide separations using various modes of high-performance liquid chromatography - PubMed
Peptide retention standards are widely used by chromatography specialists. They can be used for quality control of peptide separations (separation efficiency, selectivity, retention values) and for accurate concatenation of retention data from multiple acquisitions in proteomics. So far the repertoi ...
pubmed.ncbi.nlm.nih.gov
Spicer, V.; Krokhin, O. V., Peptide retention time prediction in hydrophilic interaction liquid chromatography. Comparison of separation selectivity between bare silica and bonded stationary phases. J Chromatogr A 2018, 1534, 75-84.
Peptide retention time prediction in hydrophilic interaction liquid chromatography. Comparison of separation selectivity between bare silica and bonded stationary phases - PubMed
1 Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada. 2 Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada.
pubmed.ncbi.nlm.nih.gov
Ogata, K.; Krokhin, O. V.; Ishihama, Y., Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS. Anal Sci 2018, 34 (9), 1037-1041.
Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS
Protein phosphorylation is one of the most ubiquitous post-translational modifications in humans, and trypsin-digested phosphorylated peptides have been analyzed by reversed phase LC/MS using C18-silica columns under acidic conditions to profile human phosphoproteomes.
www.jstage.jst.go.jp
Gussakovsky, D.; Neustaeter, H.; Spicer, V.; Krokhin, O. V. Peptide retention time prediction for immobilized artificial membrane phosphatidylcholine stationary phase: method development and preliminary observations ADMET&DMPK 2018, 6 (2) 190-199.
Peptide retention time prediction for immobilized artificial membrane phosphatidylcholine stationary phase: method development and preliminary observations
Keywords: Peptide retention modelling, immobilized artificial membrane chromatography Development of the first peptide retention prediction model for immobilized artificial membrane phosphatidylcholine (IAM.PC) stationary phase is reported. 2D LC-MS/MS analysis of a whole cell lysate of S. cerevisiae yielded a retention dataset of ~29,500 tryptic peptides; sufficient for confident assignment of retention coefficients which determine the contribution of individual amino acids in peptide retention.
pub.iapchem.org
Krokhin, O. V.; Anderson, G.; Spicer, V.; Sun, L.; Dovichi, N. J., Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis. Anal Chem 2017,
89 (3), 2000-2008.
Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis
A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies.
pubs.acs.org
Krokhin, O. V.; Ezzati, P.; Spicer, V., Peptide Retention Time Prediction in Hydrophilic Interaction Liquid Chromatography: Data Collection Methods and Features of Additive and Sequence-Specific Models. Anal Chem 2017, 89 (10), 5526-5533.
Peptide Retention Time Prediction in Hydrophilic Interaction Liquid Chromatography: Data Collection Methods and Features of Additive and Sequence-Specific Models
The development of a peptide retention prediction model for hydrophilic interaction liquid chromatography (XBridge Amide column) is described for a collection of ∼40 000 tryptic peptides. Off-line 2D LC-MS/MS analysis (HILIC-RPLC) of S. cerevisiae whole cell lysate has been used to acquire retention information for a HILIC separation.
pubs.acs.org
Gussakovsky, D.; Neustaeter, H.; Spicer, V.; Krokhin, O. V., Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography. Anal Chem 2017, 89 (21), 11795-11802.
Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography
The development of a peptide retention prediction model for strong cation exchange (SCX) separation on a Polysulfoethyl A column is reported. Off-line 2D LC-MS/MS analysis (SCX-RPLC) of S. cerevisiae whole cell lysate was used to generate a retention dataset of ∼30 000 peptides, sufficient for identifying the major sequence-specific features of peptide retention mechanisms in SCX.
pubs.acs.org
Spicer, V.; Ezzati, P.; Neustaeter, H.; Beavis, R. C.; Wilkins, J. A.; Krokhin, O. V., 3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection. Anal Chem 2016,
88 (5), 2847-55.
3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection
The growing complexity of proteomics samples and the desire for deeper analysis drive the development of both better MS instrument and advanced multidimensional separation schemes. We applied 1D, 2D, and 3D LC-MS/MS separation protocols (all of reversed-phase C18 functionality) to a tryptic digest of whole Jurkat cell lysate to estimate the depth of proteome coverage and to collect high-quality peptide retention information.
pubs.acs.org
Krokhin, O. V.; Spicer, V., Generation of accurate peptide retention data for targeted and data independent quantitative LC-MS analysis: Chromatographic lessons in proteomics. Proteomics 2016, 16 (23), 2931-2936.
Generation of accurate peptide retention data for targeted and data independent quantitative LC-MS analysis: Chromatographic lessons in proteomics - PubMed
The emergence of data-independent quantitative LC-MS/MS analysis protocols further highlights the importance of high-quality reproducible chromatographic procedures. Knowing, controlling and being able to predict the effect of multiple factors that alter peptide RP-HPLC separation selectivity is critical for successful data collection for the construction of ion libraries.
pubmed.ncbi.nlm.nih.gov
Lao, Y. W.; Gungormusler-Yilmaz, M.; Shuvo, S.; Verbeke, T.; Spicer, V.; Krokhin, O. V., Chromatographic behavior of peptides containing oxidized methionine residues in proteomic LC-MS experiments: Complex tale of a simple modification. J Proteomics 2015,
125, 131-9.
Chromatographic behavior of peptides containing oxidized methionine residues in proteomic LC-MS experiments: Complex tale of a simple modification
Hydrophobicity of Met (and oxidation products) containing peptides increases as: Mso < Msn < Met. * Oxidation decreases retention by 2.37% and 1.95% ACN for Mso and Msn, respectively. * The magnitude of retention shifts is affected by positional and secondary structure effects. * Increase of peptide hydrophobicity upon oxidation has been demonstrated for the fist time.
www.sciencedirect.com
Spicer, V.; Lao, Y. W.; Shamshurin, D.; Ezzati, P.; Wilkins, J. A.; Krokhin, O. V., N-capping motifs promote interaction of amphipathic helical peptides with hydrophobic surfaces and drastically alter hydrophobicity values of individual amino acids. Anal Chem 2014,
86 (23), 11498-502.
N-Capping Motifs Promote Interaction of Amphipathic Helical Peptides with Hydrophobic Surfaces and Drastically Alter Hydrophobicity Values of Individual Amino Acids
Capping rules, which govern interactions of helical peptides with hydrophobic surfaces, were never established before due to lack of methods for the direct measurement of polypeptide structure on the interphase boundary. We employed proteomic techniques and peptide retention modeling in reversed-phase chromatography to generate a data set sufficient for amino acid population analysis at helix ends.
pubs.acs.org
Jiang, X.; Shamshurin, D.; Spicer, V.; Krokhin, O. V., The effect of various S-alkylating agents on the chromatographic behavior of cysteine-containing peptides in reversed-phase chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2013, 915-916, 57-63.
The effect of various S-alkylating agents on the chromatographic behavior of cysteine-containing peptides in reversed-phase chromatography - PubMed
We investigate the influence of various alkylation chemistries on the reversed phase (RP) HPLC behavior of Cys-containing peptides under the most popular RP-HPLC conditions used in proteomics: C18 phases with trifluoroacetic acid (TFA) or formic acid (FA) as the ion pairing modifiers, and separation ...
pubmed.ncbi.nlm.nih.gov
Grigoryan, M.; Shamshurin, D.; Spicer, V.; Krokhin, O. V., Unifying expression scale for peptide hydrophobicity in proteomic reversed phase high-pressure liquid chromatography experiments. Anal Chem 2013, 85 (22), 10878-86.
Unifying expression scale for peptide hydrophobicity in proteomic reversed phase high-pressure liquid chromatography experiments.
As an initial step in our efforts to unify the expression of peptide retention times in proteomic liquid chromatography-mass spectrometry (LC-MS) experiments, we aligned the chromatographic properties of a number of peptide retention standards against a collection of peptides commonly observed in proteomic experiments.
europepmc.org
Krokhin, O., Peptide retention prediction in reversed-phase chromatography: proteomic applications. Expert Rev Proteomics 2012, 9 (1), 1-4.
Peptide retention prediction in reversed-phase chromatography: proteomic applications
The vast majority of proteomics analyses are performed in a bottom-up fashion, where targeted proteins are subjected to proteolytic digestion followed by reversed-phase (RP) liquid chromatography-mass spectrometry (LC-MS) analysis of the resulting peptide mixture.
www.tandfonline.com
McQueen, P.; Krokhin, O., Optimal selection of 2D reversed-phase-reversed-phase HPLC separation techniques in bottom-up proteomics. Expert Rev Proteomics 2012, 9(2), 125-8.
Optimal selection of 2D reversed-phase-reversed-phase HPLC separation techniques in bottom-up proteomics
Evaluation of: Stephanowitz H, Lange S, Lang D et al. Improved two-dimensional reversed phase-reversed phase LC-MS/MS approach for identification of peptide-protein interactions. J. Proteome Res. 11(2), 1175-1183 (2011). Recent developments in bottom-up proteomics have supplanted the use of gel-based approaches in favor of multidimensional chromatographic separations of peptide mixtures followed by mass spectrometry analysis.
www.tandfonline.com
Reimer, J.; Spicer, V.; Krokhin, O. V., Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: peptide helicity and its effect on prediction accuracy. J Chromatogr A 2012, 1256, 160-8.
Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: peptide helicity and its effect on prediction accuracy - PubMed
Twenty five years ago Houghten and DeGraw published a groundbreaking study of reversed-phase (RP)-HPLC retention of 298 peptide analogs, including 260 peptides coding the positional substitution in a 13-mer molecule with all 20 naturally occurring amino acids [1]. The authors challenged the state-of ...
pubmed.ncbi.nlm.nih.gov
Reimer, J.; Shamshurin, D.; Harder, M.; Yamchuk, A.; Spicer, V.; Krokhin, O. V., Effect of cyclization of N-terminal glutamine and carbamidomethyl-cysteine (residues) on the chromatographic behavior of peptides in reversed-phase chromatography. J Chromatogr A 2011, 1218 (31), 5101-7.
Effect of cyclization of N-terminal glutamine and carbamidomethyl-cysteine (residues) on the chromatographic behavior of peptides in reversed-phase chromatography - PubMed
N-terminal loss of ammonia is a typical peptide modification chemical artifact observed in bottom-up proteomics experiments. It occurs both in vivo for N-terminal glutamine and in vitro following enzymatic cleavage for both N-terminal glutamine and cysteine alkylated with iodoacetamide. In addition ...
pubmed.ncbi.nlm.nih.gov
Shamshurin, D.; Spicer, V.; Krokhin, O. V., Defining intrinsic hydrophobicity of amino acids' side chains in random coil conformation. Reversed-phase liquid chromatography of designed synthetic peptides vs. random peptide data sets. J Chromatogr A 2011,
1218 (37), 6348-55.
Defining intrinsic hydrophobicity of amino acids' side chains in random coil conformation. Reversed-phase liquid chromatography of designed synthetic peptides vs. random peptide data sets - PubMed
The two leading RP-HPLC approaches for deriving hydrophobicity values of amino acids utilize either sets of designed synthetic peptides or extended random datasets often extracted from proteomics experiments. We find that the best examples of these two methods provide virtually identical results--wi ...
pubmed.ncbi.nlm.nih.gov
Vu, H.; Spicer, V.; Gotfrid, A.; Krokhin, O. V., A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography. J Chromatogr A 2010, 1217 (4), 489-97.
A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography.
A model for predicting the slope (S) in the fundamental equation of linear-solvent-strength theory for peptidic compounds was developed. Our approach is based on the novel assumption that three well-defined molecular descriptors: peptide length (N), charge (Z) and hydrophobicity index (HI) are the major contributors to the value of S.
europepmc.org
Spicer, V.; Grigoryan, M.; Gotfrid, A.; Standing, K. G.; Krokhin, O. V., Predicting retention time shifts associated with variation of the gradient slope in peptide RP-HPLC. Anal Chem 2010, 82 (23), 9678-85.
Predicting Retention Time Shifts Associated with Variation of the Gradient Slope in Peptide RP-HPLC
We have developed a sequence-specific model for predicting slopes (S) in the fundamental equation of linear solvent strength theory for the reversed-phase HPLC separation of tryptic peptides detected in a typical bottom-up-proteomics experiment. These slopes control the variation in the separation selectivity observed when the physical parameters of chromatographic separation, such as gradient slope, flow rate, and column size are altered.
pubs.acs.org
Krokhin, O. V.; Spicer, V., Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal Chem 2009
, 81 (22), 9522-30.
Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides
The growing utility of peptide retention prediction in proteomics would benefit from the development of a universal peptide retention standard for better alignment of chromatographic data obtained using various liquid chromatography (LC) platforms. We describe a six-peptide mixture designed for this purpose; its members cover a wide range of hydrophobicity for the most popular modes of reversed-phase peptide high-performance liquid chromatography (HPLC): C18 sorbents with trifluoroacetic/formic acid as the ion-pairing modifier and separations at pH 10.
pubs.acs.org
Dwivedi, R. C.; Spicer, V.; Harder, M.; Antonovici, M.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V., Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 2008, 80 (18), 7036-42.
Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics
We describe the practical implementation of a new RP (pH 10 − pH 2) 2D HPLC−ESI/MS scheme for large-scale bottom-up analysis in proteomics. When compared to the common SCX-RP approach, it provides a higher separation efficiency in the first dimension and increases the number of identified peptides/proteins.
pubs.acs.org
Tripet, B.; Cepeniene, D.; Kovacs, J. M.; Mant, C. T.; Krokhin, O. V.; Hodges, R. S., Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location. J Chromatogr A 2007, 1141 (2), 212-25.
Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location - PubMed
The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at ...
pubmed.ncbi.nlm.nih.gov
Spicer, V.; Yamchuk, A.; Cortens, J.; Sousa, S.; Ens, W.; Standing, K. G.; Wilkins, J. A.; Krokhin, O. V., Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. Anal Chem 2007, 79 (22), 8762-8.
Sequence-Specific Retention Calculator. A Family of Peptide Retention Time Prediction Algorithms in Reversed-Phase HPLC:  Applicability to Various Chromatographic Conditions and Columns
Separation selectivity of C18 reversed-phase columns from different manufacturers has been compared to evaluate the applicability of our sequence-specific retention calculator (SSRCalc) peptide retention prediction algorithms. Three different versions of SSRCalc are currently in use:  300-Å pore size sorbents (TFA as ion-pairing modifier, pH 2), 100 Å (TFA, pH 2), and 100 Å (pH 10), which have been applied for the separation of randomly chosen mixture of tryptic peptides.
pubs.acs.org
Krokhin, O. V.; Antonovici, M.; Ens, W.; Wilkins, J. A.; Standing, K. G., Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: Consequences for MALDI and HPLC-MALDI analysis. Anal Chem 2006, 78 (18), 6645-50.
Deamidation of -Asn-Gly- Sequences during Sample Preparation for Proteomics:  Consequences for MALDI and HPLC-MALDI Analysis
We find that peptides containing -Asn-Gly- sequences typically show ∼70−80% degree of deamidation after standard overnight (∼12 h) tryptic digestion at 37 °C. This emphasizes the need for more detailed information about the deamidation reaction in -Asn-Gly- sequences, in which two deamidated species are produced, one containing an aspartic acid (-Asp-Gly-) residue and the other containing an isoaspartic acid (-βAsp-Gly-) residue.
pubs.acs.org
Krokhin, O. V.; Ying, S.; Cortens, J. P.; Ghosh, D.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A., Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal Chem 2006, 78 (17), 6265-9.
Use of Peptide Retention Time Prediction for Protein Identification by off-line Reversed-Phase HPLC−MALDI MS/MS
A new algorithm, sequence-specific retention calculator, was developed to predict retention time of tryptic peptides during RP HPLC fractionation on C18, 300-Å pore size columns. Correlations of up to ∼0.98 R2 value were obtained for a test library of ∼2000 peptides and ∼0.95−0.97 for a variety of real samples.
pubs.acs.org
Krokhin, O. V., Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal Chem 2006, 78 (22), 7785-95.
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-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).
pubs.acs.org
Krokhin, O. V.; Craig, R.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A., An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol Cell Proteomics 2004, 3 (9), 908-19.
An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC
The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560- to 4,000-Da mass range, derived from a mixture of 17 protein digests.
www.mcponline.org
