Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap*S

By Jesper V. Olsen, Lyris M. F. de Godoy, Guoqing Li, Boris Macek, P. Mortensen, R. Pesch, A. Makarov, Oliver Lange, S. Horning, Matthias Mann. Molecular & Cellular Proteomics, 2005

1,514 citations recorded by the source corpus.

Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers are well controlled. Here we demonstrate sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap (C-trap) to the orbitrap mass spectrometer (LTQ Orbitrap). Prior to acquisition of a spectrum, a background ion originating from ambient air is first transferred to the C-trap. Ions forming the MS or MSn spectrum are then added to this species, and all ions are injected into the orbitrap for analysis. Real time recalibration on the “lock mass” by corrections of mass shift removes mass error associated with calibration of the mass scale. The remaining mass error is mainly due to imperfect peaks caused by weak signals and is addressed by averaging the mass measurement over the LC peak, weighted by signal intensity. For peptide database searches in proteomics, we introduce a variable mass tolerance and achieve average absolute mass deviations of 0.48 ppm (standard deviation 0.38 ppm) and maximal deviations of less than 2 ppm. For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching. High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/644cc7f6990bf3a02e3bcb48930eb9cbf9ed6c03

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Citations in the corpus

A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods. (2015, methodology): “Real-time recalibration is performed using a background ion from ambient air in the C-trap [25].”
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ (2014, methodology): “Each fraction was purified with C18 StageTips (46) and analyzed via liquid chromatography combined with electrospray tandem mass spectrometry on an LTQ Orbitrap (Thermo Fisher) with lock mass calibration (47).”
A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles (2011, methodology): “A lock mass ion from ambient air (m/z 445.120025) was used for internal calibration of all measurements in the Orbitrap (23).”
Proteomics by mass spectrometry: approaches, advances, and applications. (2009, background): “There are several papers that review and benchmark the performance of the Orbitrap for bottom-up (32, 33, 35, 56, 57) and top-down (58, 59) proteomic applications.”
Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome (2008, background): “The rapid improvements in MS instrumentation, exemplified by the linear ion trap triple quadropole (LTQ) Fourier transform ion cyclotron resonance and LTQ-Orbitrap instruments, now facilitate a high throughput PTM analysis [31–35].”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “This question is particularly relevant in the case of high mass accuracy instruments such as LTQ-Orbitrap, where performing searches with very narrow mass tolerance is an attractive option [206].”
Analysis and validation of proteomic data generated by tandem mass spectrometry (2007, background): “Although it is possible to take into account auxiliary information in the threshold-based approache”
Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* (2012, neutral): “parts-per-million (ppm) mass measurement error routine (54).”