SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments

Abstract

While the performance of liquid chromatography (LC) and mass spectrometry (MS) instrumentation continues to increase, applications such as analyses of complete or near-complete proteomes and quantitative studies require constant and optimal system performance. For this reason, research laboratories and core facilities alike are recommended to implement quality control (QC) measures as part of their routine workflows. Many laboratories perform sporadic quality control checks. However, successive and systematic longitudinal monitoring of system performance would be facilitated by dedicated automatic or semiautomatic software solutions that aid an effortless analysis and display of QC metrics over time. We present the software package SIMPATIQCO (SIMPle AuTomatIc Quality COntrol) designed for evaluation of data from LTQ Orbitrap, Q-Exactive, LTQ FT, and LTQ instruments. A centralized SIMPATIQCO server can process QC data from multiple instruments. The software calculates QC metrics supervising every step of data acquisition from LC and electrospray to MS. For each QC metric the software learns the range indicating adequate system performance from the uploaded data using robust statistics. Results are stored in a database and can be displayed in a comfortable manner from any computer in the laboratory via a web browser. QC data can be monitored for individual LC runs as well as plotted over time. SIMPATIQCO thus assists the longitudinal monitoring of important QC metrics such as peptide elution times, peak widths, intensities, total ion current (TIC) as well as sensitivity, and overall LC-MS system performance; in this way the software also helps identify potential problems. The SIMPATIQCO software package is available free of charge.

Figure 1

Components and flow of information using SIMPATIQCO. Two types of QC samples are analyzed on each LC–MS system: QC 1 contains a simple digested protein mixture (e.g., cytochrome c, BSA, and synthetic phosphopeptides) that is measured 1–2×/day for an evaluation of sensitivity and LC metrics such as peptide retention times. QC 2 is a HeLa digest that is analyzed 1–2×/week to evaluate system speed and overall performance. After upload of the respective raw files to the SIMPATIQCO server, QC metrics are calculated and stored in a PostgreSQL database. The database is linked to a webserver and can be queried to visualize the time course of QC metrics via a web browser.

Figure 2

Example of SIMPATIQCO output: BSA sequence coverage (A) and average MS¹ ion injection times (B) on a Velos Orbitrap system monitored over time. System maintenance and service messages were entered manually by an operator and illustrate the relationship between the two QC metrics and system maintenance efforts such as venting and cleaning of the S-lens and exit lens (log entry “S-lens cleaned”) by laboratory staff (which improved BSA sequence coverage but led to an only transient reduction in average MS¹ injection times) or venting and cleaning of the transfer lens between the high pressure and the low pressure cells by a service engineer. Green band: within 1 × median absolute deviation (MAD). Yellow: 1–2 × MAD. Red: outside 2 × MAD.

Figure 3

Lock mass deviation from a QC 1 sensitivity run (CID): peculiar pattern, plateaus indicate that lock mass was not detected (A). TIC from a QC 2 performance run (ETD): considerable fraction of TIC between 180 and 200 min (B). Different QC 2 performance run (ETD): PSMs per minute (C) and m/z of triggered precursors (D) plotted over the entire retention time range of the raw file.