SIEVE User Guide

Understanding the ChromAlign Process
When you send an experiment for analysis after selecting sample and control files and setting
parameters, SIEVE performs an automatic aligning process called ChromAlign 1 . This process
aligns the chromatograms of the sample files with the first control file, correcting
chromatographic shifts. The following factors can contribute to chromatographic shifts,
which are part of the challenge in biomarker discovery driven by differential analysis:
• The difficulty in reproducing LC/MS experiments
• Aging of separation columns, changes in sample buffer or content, or fluctuations in
temperature and sample flow
• The absence of any prediction model that explains peptide elution in chromatographic
columns and allows alignment of eluting peaks through the accurate modeling of peptide
elution.
The following sections provide detailed information about the ChromAlign process:
• Outlining the ChromAlign Process
• Starting the ChromAlign Process
• ChromAlign First Level Alignment
• ChromAlign Second Level Alignment
• Aligning Over Different Abundance Levels
• Aligning Over Chromalign Time Shifts
1 ChromAlign: US Patent applied for.
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