Thermo Fisher Scientific Introduces Peptide Calibration Reagent to Optimize Liquid Chromatography Performance

"Thermo Fisher Scientific, the world leader in serving science, today announced the availability of the Thermo Scientific Pierce Peptide Retention Time Calibration Mixture for the prediction of peptide retention times on reversed-phase high-performance liquid chromatography (HPLC) columns. 
The convenient, ready-to-use Pierce® Peptide Retention Time Calibration Mixture contains 15 synthetic, heavy peptides mixed at an equimolar ratio to elute across the chromatographic gradient. It can be used with Thermo Scientific Pinpoint Software to predict peptide retention time from sequence alone, using hydrophobicity factors, or to predict peptide retention time between instrument platforms. 

The Pierce Peptide Retention Time Calibration Mixture streamlines the transition from qualitative protein discovery results to the development of targeted mass spectrometry (MS) assays on Thermo Scientific Triple Quadrupole, Orbitrap and Exactive Instruments and all other mass spectrometers. It also saves time in peptide purification by increasing the prediction efficiency of peptide retention profiles. The mixture is useful in evaluating different reversed-phase column and gradient options, monitoring for autosampler and HPLC column performance characteristics and normalizing results between experiments and over time."

peptide retention time

Is peptide RT charge specific?
"Not in the sense that ESI-charge is influencing the retention time but
in the sense that longer peptide tend to elute later in the
chromatogram and also are more likely to have higher charge states,
there is a slight correlation between charge state and retention time.
however it would work as prediction tool if you consider predicting
the charge state of a peptide, which is actually not that difficult to
do." by Hannes.

BMC Genomics. 2010 Dec 1;11 Suppl 3:S8.

ICPD-a new peak detection algorithm for LC/MS.

Zhang J, Haskins W.

Department of Electrical Engineering, University of Texas at San Antonio, Texas, USA. michelle.zhang@utsa.edu

Abstract

BACKGROUND: The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise and sample variability, whose statistical characteristics are still elusive, making computational identification of low abundance proteins extremely challenging. As a result, the inability of identifying low abundance proteins in a proteomic study is the main bottleneck in protein biomarker discovery.

RESULTS: In this paper, we propose a new peak detection method called Information Combining Peak Detection (ICPD ) for high resolution LC/MS. In LC/MS, peptides elute during a certain time period and as a result, peptide isotope patterns are registered in multiple MS scans. The key feature of the new algorithm is that the observed isotope patterns registered in multiple scans are combined together for estimating the likelihood of the peptide existence. An isotope pattern matching score based on the likelihood probability is provided and utilized for peak detection.

CONCLUSIONS: The performance of the new algorithm is evaluated based on protein standards with 48 known proteins. The evaluation shows better peak detection accuracy for low abundance proteins than other LC/MS peak detection methods.