--- title: "The Lab Savior: A Comprehensive HPLC Troubleshooting Guide" description: Stuck with high back pressure or tailing peaks? Follow our HPLC troubleshooting guide covering mobile phase, pump, injector, column, and detector. image: https://blog.seqgen.com/hubfs/hplc-troubleshooting-sketchnote.png --- - [MARKETPLACE](https://seqgen.com/marketplace/) - [CAREERS](https://seqgen.com/careers/) - [TERMS & CONDITIONS](https://seqgen.com/wp-content/uploads/2026/03/POL_011-Rev.A_Terms-and-Conditions-of-Sales-for-Products-and-Services.pdf) - [ISO 9001 CERTIFICATE](https://seqgen.com/wp-content/uploads/2026/01/SeqGen-Final-Cert_2026-2029.pdf) - [SALES INQUIRY](https://seqgen.com/sales-inquiry/) - [SERVICE REQUEST](http://seqgen.com/service-request/) - [TESTIMONIALS](https://seqgen.com/testimonials/) [![SeqGen](https://seqgen.com/wp-content/uploads/2020/03/seqgen_logo.png)](https://seqgen.com/) - [SeqMo Rewards](https://seqgen.com/seqmo-rewards/) - [HOME](https://seqgen.com/) - [ABOUT US](https://seqgen.com/about-us/) - [Our History](https://seqgen.com/about-us/our-history-2/) - [Our Engineers](https://seqgen.com/about-us/our-engineers/) - 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[ISO 9001 CERTIFICATE](https://seqgen.com/wp-content/uploads/2026/01/SeqGen-Final-Cert_2026-2029.pdf) # The Lab Savior: A Comprehensive HPLC Troubleshooting Guide 09 March 2026 [LC-MS](https://blog.seqgen.com/topic/lc-ms) [0](https://blog.seqgen.com/the-lab-savior-a-comprehensive-hplc-troubleshooting-guide#comments-listing) ## Quick-Start Diagnostic Summary  If you are currently facing an instrument issue, follow this logical flow to isolate the source: **Mobile Phase → Pump → Injector/Autosampler → Column → Detector**.   - **No Signal?** Verify the detector lamp is ON, check the wavelength setting, and purge the pump to remove air.  - **Pressure Anomalies?** High pressure usually indicates a blocked frit or column; low pressure often suggests a leak or air in the pump heads. - **Peak Shape Issues?** Address split peaks by replacing the guard column; resolve fronting by reducing injection volume; check fittings for dead volume if peaks are tailing.  - **Retention Time (RT) Shifts?** Stabilize the column oven temperature and ensure the mobile phase is fresh and degassed. - **Expert Maintenance:** [Contact SeqGen](https://seqgen.com/service-request/) for persistent Sciex MS sensitivity loss, internal Shimadzu failures, or annual Preventive Maintenance (PM)/compliance requirements.  ###### [Watch the summary on our YouTube blog channel](https://youtu.be/cKy64AdIk5M) In the daily routine of High-Performance Liquid Chromatography (HPLC) analysis, instrument "hiccups" are almost a rite of passage for every lab technician. Whether it’s an erratic baseline, pressure spikes, or collapsing peak shapes, these issues don’t just delay your workflow—they compromise the integrity of your data. At SeqGen, we understand that downtime is the enemy of productivity. We’ve compiled this expert troubleshooting guide based on years of experience with Sciex and Shimadzu systems to help you identify and resolve common issues quickly. We recommend bookmarking this page as a standard reference for your lab bench. ## The Golden Rule of HPLC Troubleshooting When a problem arises, don't panic. Follow this logical flow to isolate the source: Mobile Phase → Pump → Injector/Autosampler → Column → Detector.  By following this sequence, you can systematically rule out variables and pinpoint the exact cause of your hardware "hiccup". Let’s start with the most common scenarios you'll face at the bench:  ##### 1. No Peak / No Signal This is the most alarming scenario, but it is often related to basic setup or connectivity. - **Possible Causes:** Detector lamp is OFF or weak; wrong wavelength setting; no actual injection occurred; pump is not delivering mobile phase due to air bubbles. - **Quick Solutions:** Verify detector lamp status and wavelength. - Confirm injection volume in the software. - Purge the pump thoroughly to remove air. - Check the pressure reading; if it’s 0, verify solvent levels and check for disconnected tubing.   ##### 2. Peak Shape Issues: Split, Fronting, or Tailing - **Split Peaks:** Usually caused by a column void or a contaminated guard column. Try flushing the column or replacing the guard column. Ensure your sample diluent matches your mobile phase. - **Fronting Peaks:** Often a sign of column overload. Reduce your injection volume or dilute your sample concentration. - **Tailing Peaks:** The most common headache. This usually stems from column contamination, improper pH (active silanol interactions), or dead volume in the fittings. - *Tip:* Check all connections. Even a microscopic gap in a fitting can cause significant tailing.   ##### 3. Pressure Anomalies: High vs. Low - **High Back Pressure:** Indicates a blockage. Check the column frit, guard column, or look for microbial growth in aqueous mobile phases. - *Action:* Flush the system (Water → IPA/ACN) or reverse-flush the column if the manufacturer allows. - **Low Pressure / Fluctuations:** Typically caused by a leak or air in the pump heads. Tighten loose fittings and check the pump seals. If pressure pulses, your check valves may need cleaning or replacement. ##### 4. Baseline Noise & Retention Time Shift - **Baseline Noise:** Often due to air bubbles, dirty solvents, or a lamp reaching the end of its lifespan. Ensure all mobile phases are properly degassed and filtered. - **RT Shift:** This usually points to a change in flow rate or mobile phase composition (e.g., evaporation of organic modifiers). Ensure your column oven temperature is stable and your pump is calibrated.   ## When Should You Contact SeqGen? While the steps above resolve 80% of routine issues, certain deep-seated technical failures require professional intervention. It may be time to call in the experts if you encounter: - Persistent sensitivity loss in Sciex MS systems that cleaning the interface won't fix. - Internal leaks or motor failures within Shimadzu units. - Complex synchronization errors between the LC and the Mass Spec. - Annual PM or IQ/OQ/PQ certification requirements. At SeqGen, we specialize in keeping your legacy and high-end systems running like new. Our goal is to ensure your research never stops due to equipment failure. If you’ve followed this guide and the problem persists, our technical team is ready to assist. ## HPLC Troubleshooting Cheat Sheet Quick Diagnostic Flow: Mobile Phase → Pump → Injector/Autosampler → Column → Detector. **Problem: Peak Shape & Retention** | **Symptom** | **Common Causes** | **Immediate Action** | | --- | --- | --- | | **Split Peaks** | Column void; Contaminated guard column; Solvent mismatch. | Replace guard column; Ensure sample diluent matches mobile phase. | | **Tailing Peaks** | Active silanol sites; Dead volume; Column contamination. | Adjust pH; Check/tighten all fittings; Flush column with strong solvent. | | **Fronting Peaks** | Column overload; Sample concentration too high. | Reduce injection volume; Dilute sample. | | **RT Shift** | Flow rate change; Temperature fluctuation; Air in pump. | Check for leaks; Stabilize column oven; degas mobile phase. |   **Problem: Pressure & Flow** | **Symptom** | **Common Causes** | **Immediate Action** | | --- | --- | --- | | **High Pressure** | Blocked frit; Plugged column; Precipitated buffer. | Replace guard column/frit; Flush with 100% water (if buffer) then organic. | | **Low Pressure** | Leak in system; Loose fitting; Pump seal failure. | Tighten fittings; Inspect pump for leaks; Prime pump heads. | | **Cycling Pressure** | Air bubble in pump; Faulty check valve. | Purge/Prime pump; Sonicate check valves in IPA. |   **Problem: Baseline & Signal** | **Symptom** | **Common Causes** | **Immediate Action** | | --- | --- | --- | | **No Signal** | Lamp OFF; Wrong wavelength; No injection. | Check lamp energy; Verify λ; Confirm autosampler needle stroke. | | **Baseline Noise** | Air bubbles; Lamp aging; Dirty mobile phase. | Degas solvents; Replace lamp; Filter all mobile phases (0.22μm). | | **Baseline Drift** | Temperature change; Column bleed; Slow equilibration. | Monitor column oven; Increase equilibration time. | For a faster diagnostic flow you can keep at your bench, refer to our visual summary below—designed to help you isolate issues from mobile phase to detector at a glance.  ## ![HPLC Troubleshooting Guide Sketchnote](https://blog.seqgen.com/hs-fs/hubfs/hplc-troubleshooting-sketchnote.png?width=668&height=373&name=hplc-troubleshooting-sketchnote.png)*The SeqGen HPLC Troubleshooting Cheat Sheet Sketchnote.*   ## Maintenance & Prevention Checklist Resolving an immediate issue is only half the battle; staying ahead of hardware wear and tear is the key to consistent data. Use the following checklist to build a robust preventative routine in your lab:  - **Daily:** Check solvent levels; degas mobile phase; check for leaks. - **Weekly:** Flush system with 100% Organic (ACN/IPA) to prevent microbial growth. - **Monthly:** Inspect pump seals and check valve performance. - **Annual:** Schedule a SeqGen PM to ensure hardware longevity and IQ/OQ compliance.    ## **Technical Support** If troubleshooting steps do not resolve the issue, or for Sciex/Shimadzu specific hardware failures, please contact our technical support team: - Website: [seqgen.com](http://www.seqgen.com) - Service request: [seqgen.com/service-request/ ](https://seqgen.com/service-request/) - Email: service@seqgen.com   ---   SeqGen specializes in the repair, maintenance, and refurbishment of essential laboratory instruments used in DNA sequencing and genetic research. 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