Performance Comparisons of Nano-LC Systems, Electrospray Sources and LC–MS-MS Platforms

Abstract

Selecting a suitable nano-liquid chromatography system (LC), ionization source and mass spectrometer for LC-tandem mass spectrometry (MS-MS) studies is complicated by numerous competing technologies. This study compares four popular nano-LC systems, four ionization sources and three MS facilities that use completely different LC-MS-MS systems. Statistically significant differences in LC performance were identified with similarly performing Proxeon, Waters and Eksigent nanoLC-Ultra systems [retention time routinely at 0.7-0.9% relative standard deviation (RSD)], and all outperformed the Eksigent nanoLC-2D (RSD ∼2%). In addition, compatibility issues were identified between the Bruker HCT ion trap mass spectrometer and both the Eksigent nanoLC-2D and the Bruker nanoelectrospray source. The electrospray source itself had an unexpected and striking effect on chromatographic reproducibility on the Bruker HCT ion trap. The New Objective nanospray source significantly outperformed the Bruker nanospray source in retention time RSD (1% RSD versus 14% RSD, respectively); and the Bruker nebulized nanospray source outperformed both of these traditional, non-nebulized sources (0.5% RSD in retention time). Finally, to provide useful benchmarks for overall proteomics sensitivity, different LC-MS-MS platforms were compared by analyzing a range of concentrations of tryptic digests of bovine serum albumin at three MS facilities. The results indicate that similar sensitivity can be realized with a Bruker HCT-Ultra ion trap, a Thermo LTQ-Velos Linear ion trap and a Thermo LTQ-Orbitrap XL-ETD.

Towards a rapid identification and a novel proteomic analysis for dermatophytes from human and animal dermatophytosis

“…Ongoing improvements in proteomics innovation display new scope for clinical implementations in specialised laboratories or hospitals including the novel biomarkers discovery, protein identification, monitoring of disease, and detecting drugs adverse effects and environmental hazards . Technologies applied in proteomics depends upon liquid chromatography (LC) coupled to nano‐electrospray ionisation MS (nano‐ESI‐MS) and tandem MS for determining protein/peptide sequences and molecular composition . Nano‐ESI‐MS provides a sensitive, robust and dependable device for examining organisms, at femto‐mole amounts in micro‐litre sample volumes that are not amenable to examination by other conventional methods…”

“…6 Technologies applied in proteomics depends upon liquid chromatography (LC) coupled to nano-electrospray ionisation MS (nano-ESI-MS) and tandem MS for determining protein/peptide sequences and molecular composition. 7 Nano-ESI-MS provides a sensitive, robust and dependable device for examining organisms, at femto-mole amounts in micro-litre sample volumes that are not amenable to examination by other conventional methods. 8 It is obvious that dermatophytes proteases are paramount for its virulence, causing tissue damage and impairment of immunity, since these Arthrodermataceae develop only in the stratum corneum, nails or hair, which establishes their sole nitrogen and carbon sources.…”

Assessing a commercial capillary electrophoresis interface (ZipChip) for shotgun proteomic applications

“…The maximum time variation across runs is shown and approximated a 16 second shift in apex peak elution time. When compared to a recent analysis of repeated runs of a BSA digest standard on 4 different nlC systems 22 the zCE-MS separation appears comparable.…”

Peptidomic Approach for the Identification of Peptides with Potential Antioxidant and Anti-Hyperthensive Effects Derived From Asparagus By-Products

“…Such retention time driftings are indeed acceptable for nanoHPLC-MS analysis. Retention time drifting is a well-known phenomenon that negatively affects proteomics and metabolomics dataset alignment [33] and can be caused by several factors, such as the conditions and the aging of the chromatographic column and the temperature fluctuations [34,35].…”