HPLC LC/MS Troubleshooting

Chromatography troubleshooting is a key part of a chromatographer’s daily work. Here, we present articles and protocols to help a chromatorgher achieve this efficiently.

Two panels contrasting baseline noise, a fast random jitter pointing to the detector or mobile phase, with baseline drift, a slow directional shift pointing to temperature, gradient or refractive-index effects, or the column.

HPLC Baseline Noise and Drift: How to Tell Them Apart and Fix Each

An unstable baseline is one of the most common — and most time-consuming — problems in HPLC; by some estimates, baseline issues account for 30–40% of the troubleshooting time in an analytical lab. A wandering or fuzzy baseline masks low-level peaks, degrades your signal-to-noise ratio, and quietly pushes up your detection limits. But “my baseline …

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Gradient blank chromatogram with a rising percent-B line above small ghost peaks that elute as the organic gradient increases even though no sample was injected.

Ghost Peaks in HPLC: What Causes Them and How to Eliminate Them

You inject a blank — pure solvent, no sample — and peaks appear anyway. Or your gradient runs show extra peaks that aren’t in your standards, drifting in and out from one sequence to the next. These are ghost peaks (also called artifact or system peaks): signals that don’t come from your sample. They masquerade …

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Post-column infusion trace showing ion suppression dips where matrix components co-elute, with the analyte retention time overlapping a suppression zone.

Losing Sensitivity in LC-MS? A Systematic Guide to Ion Suppression and Signal Loss

Few problems in the LC-MS lab are as demoralizing as watching your signal quietly disappear. A method that gave clean, intense peaks last month now barely clears the noise — same sample, same instrument, no obvious change. Because an LC-MS signal depends on the entire chain from sample prep through chromatography to ionization and detection, …

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Comparison of a symmetric HPLC peak with asymmetry factor near 1.0 versus a tailing peak with tailing factor above 1.5, showing the slow tail from secondary retention or dead volume.

Why Your HPLC Peaks Are Tailing: Causes and a Diagnostic Path

Peak tailing is one of the most common complaints in HPLC — and one of the most misdiagnosed. A tailing peak inflates integration error, degrades resolution, and can quietly fail a system suitability requirement. But “my peaks are tailing” isn’t a diagnosis; it’s a starting point. The same asymmetric peak can come from silanol interactions, …

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Diagram of the HPLC flow path from pump through injector, guard column, analytical column, and detector, illustrating sequential disconnection to locate a backpressure restriction.

High Backpressure in HPLC: 8 Root Causes and How to Diagnose Each One

High system backpressure is one of the most common — and most disruptive — problems in liquid chromatography. It interrupts runs, triggers pump shutoffs, and at worst forces you to scrap a column mid-sequence. The frustrating part is that “high pressure” is a symptom, not a diagnosis. The same 600 bar reading can come from …

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Understanding Size Exclusion Chromatography Techniques

If you’re delving into the world of chromatography, you might have come across a technique called size exclusion chromatography (SEC). This method is essential for separating molecules based on their size, and it plays a crucial role in various scientific fields. In this article, we’ll explore everything you need to know about size exclusion chromatography, …

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Understanding RF Values in Chromatography Techniques

Chromatography is a powerful tool in chemistry. It helps separate and identify compounds in a mixture. A key concept in chromatography is the RF value. RF stands for Retention Factor. It is a dimensionless number used to describe the movement of a compound on a chromatography medium. Understanding RF values is crucial for interpreting chromatographic …

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How to Develop an HPLC Method: A Step-by-Step Practical Guide

Introduction Developing an HPLC method is one of the most fundamental skills in analytical chemistry. Whether working in pharmaceutical analysis, bioanalysis, environmental testing, or QC laboratories, a structured approach to method development saves time, improves reproducibility, and strengthens regulatory defensibility. Yet many scientists still rely on trial-and-error adjustments instead of systematic strategy. This guide outlines …

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Understanding Chromatography Resins: A Comprehensive Guide

Title Tag: Chromatography Resin Guide: Types & Applications Chromatography resins are vital in the world of separation science. They play a key role in purifying biomolecules. These resins are used in various chromatography techniques. Each technique has its unique application and benefits. Resin column chromatography is a popular method. It involves packing resins into a …

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