Quantitative proteomics of rat and human pancreatic beta cells.

Data set description: This data set is composed by label-free alternate-scanning LC-MS/MS proteomics analysis human and Wistar rat pancreatic islet endocrine cells. The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat). From these mass spectrometry data, 'relative molar amount units' between cell types and across species were calculated. Biological relevance: These data provide a quantitative view on the unfractionated proteomes of human and rat beta and alpha cells. It is likely biased towards the proteins with higher molar abundance, relating to core functional pathways, but also includes several proteins with an islet-enriched expression. The quality of the cell preps is state-of-the-art, and the label-free quantitation is both precise and accurate, allowing detailed quantitative analysis.

Surface and wastewater quality monitoring: combination of liquid chromatography with (geno)toxicity detection, diode array detection and tandem mass spectrometry for identification of pollutants.

Identification of unknown water pollutants with liquid chromatography and tandem mass spectrometry (LC-MS-MS) is often more complex and time consuming than identification with gas chromatography and mass spectrometry (GC-MS). In order to focus the identification effort on relevant compounds, unknown peaks need to be selected carefully. Based on its frequency of occurrence in the LC-Diode Array Detection (LC-DAD) chromatograms of surface and infiltrated waters, an unknown peak was selected for identification with LC-MS-MS. This compound was identified as hexamethoxymethylmelamine (HMMM), a chemical often used in the coating industry. This is the first time the presence of this chemical in surface waters has been reported. In addition to HMMM, two other structurally related compounds were found to be present in the investigated surface water. A standard mixture of HMMM and its by-products did not exhibit (geno)toxicity under the test conditions applied in this study. In another example, a genotoxic fraction of an industrial wastewater was isolated and examined by LC-MS-MS using a modern quadrupole-orthogonal acceleration-time-of-flight mass spectrometer (Q-TOF). Four compounds were detected. The structures of two compounds present are proposed to be 9-amino-2-hydroxy-acridine and 9-hydroxy-acridine-N-oxide or its structural isomer dihydroxy-acridine. Confirmation with standards could not be carried out, as pure compounds are not available. The other two compounds (structural isomers) could not be identified based on the data available within this study.

A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation.

A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H3PO4) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation.

Screening and identification of unknown contaminants in water with liquid chromatography and quadrupole-orthogonal acceleration-time-of-flight tandem mass spectrometry.

In order to assess and maintain the quality of surface waters, target compound monitoring is often not sufficient. Many unknown micro-contaminants are present in water, originating in municipal, industrial or agricultural effluents. Some of these might pose a risk to drinking water production and consequently to human health. The possibilities of screening surface water and identification of these non-target water pollutants with modern data acquisition possibilities of hybrid quadrupole-orthogonal acceleration time of flight mass spectrometers (Q-TOF), such as data-dependent MS to MS/MS switching were investigated. Using model compounds, a procedure for the liquid chromatography-tandem mass spectrometry (LC-MS/MS) screening of water extracts was developed, enabling the detection and identification of compounds at levels < or = 0.25 microg/l in surface water. Based on the accurate mass the elemental compositions for the precursor and product ions are calculated. The calculated chemical formulae are searched against the Merck index, the NIST library, an own database containing about 2,500 water pollutants (pesticides and other contaminants) as well as a CI-CID library containing tandem MS spectra of about 100 water contaminants. The developed approach was applied for the identification of unknown compounds, present in native surface water extract. For three of these compounds, structures were proposed. Confirmation of the proposed structures with standards was beyond the scope of this study.

Screening for anabolic steroids and related compounds in illegal cocktails by liquid chromatography/time-of-flight mass spectrometry and liquid chromatography/quadrupole time-of-flight tandem mass spectrometry with accurate mass measurement.

Findings of illegal hormone preparations such as syringes, bottles, cocktails, and so on, are an important information source for the nature of the current abuse of anabolic steroids and related compounds as growth-promoting agents in cattle. A new screening method for steroids in cocktails is presented based on liquid chromatography (LC) with diode-array UV-absorbance detection and electrospray ionization time-of-flight mass spectrometry (ESI-TOFMS). Accurate mass measurements were performed at a mass resolution of 4000 using continuous introduction of a lock mass through a second (electro)sprayer. Similar experiments were carried out using dual-sprayer quadrupole time-of-flight mass spectrometry (ESI-QTOFMS/MS) at a mass resolution of 10 000 with data-dependent MS/MS acquisition; i.e. beyond an intensity threshold for the [M + H](+) ions, MS/MS spectra were automatically acquired at three different collision energies. Elemental compositions were calculated for precursor and product ions and it is shown that the combined information from LC retention behavior, UV spectra, elemental compositions, and accurate mass MS/MS spectra yield a fast impression of the steroids present in the complex mixture. Using a new software tool for structure elucidation of MS/MS spectra, an additional non-steroidal additive was identified as well.

Hydrodynamic aspects of slurry packing processes in microcolumn liquid chromatography.

A Stokesian dynamics computer simulation based method is presented for the estimation of the bed porosity of slurry-packed capillary liquid chromatography (LC) columns. A colloidally well-described reversed-phase stationary phase-slurry liquid suspension was used as a model system. The applied simulation method takes into account the velocity of the slurry and colloidal interaction forces, as well as inter-particle hydrodynamic interactions. The predicted bed porosities suggest that a lower slurry velocity leads to a denser packing structure due to the increased effect of colloidal repulsion effects. The results of the simulations were compared with the external porosity and chromatographic performance of capillary LC columns that were packed at different filtration and compaction pressures. However, the trends that were observed in the experimental results suggest that hydrodynamic packing parameters have no or little effect on the chromatographic performance of capillary LC columns. Within the experimental parameter window, the chromatographic performance and the column porosity were not influenced by the filtration and compaction pressure, nor by the duration of the compaction process.

Recent developments in microcolumn liquid chromatography.

An overview of the most recent developments in microcolumn liquid chromatography (LC) is presented. A short theoretical discussion on chromatographic dilution and extracolumn bandbroadening is given and also the recent progress and advances in column technology and instrumentation are reviewed. However, the emphasis of this review is on miniaturized sample clean-up, sample introduction techniques and on both established and more recent detection techniques for microcolumn LC. The hyphenation of miniaturized LC columns with other techniques, specifically on multidimensional chromatography and the coupling of microcolumn LC to mass spectrometry is discussed in detail. Both the on-line and automated off-line interfacing to other separation and detection techniques will also be addressed. Finally, a number of typical microcolumn LC applications are presented in order to demonstrate the potential of microcolumn LC methods in a variety of scientific areas.

Automated on-line ionic detergent removal from minute protein/peptide samples prior to liquid chromatography-electrospray mass spectrometry.

An automated on-line ionic detergent removal pre-column system coupled to capillary liquid chromatography-electrospray mass spectrometry is described. The system involves two micro precolumns, composed of a specific ionic detergent trapping column and a preconcentration column, respectively, and a packed 300 microns I.D. analytical column. Sample loading to the micro precolumns and regeneration of the detergent trapping column were performed at a flow-rate of 50 microliters/min, while the flow-rate through the analytical column was set at 5.0 microliters/min. Ionic detergent-containing tryptic-digested protein samples were directly applied to the micro precolumns without sample pretreatment and were analysed by UV absorption detection and electrospray mass spectrometry. The presented system allows for the fully automated removal of SDS with virtually no loss in protein/peptides. Maximum SDS load and breakthrough have been determined. Excellent protein recovery and complete removal of SDS is found. The chromatographic separation after SDS removal was completely restored and equalled the reference chromatogram. Mass spectral data confirm these findings. Finally, this technique allows for SDS removal from minute protein samples without the need for any sample handling.

Sodium dodecyl sulphate removal from tryptic digest samples for on-line capillary liquid chromatography/electrospray mass spectrometry.

An on-line microcolumn switching method was developed for the removal of sodium dodecyl sulphate (SDS) from tryptic digest samples. The system includes two micro-precolumns: a specific ionic detergent trapping column and a preconcentration column. Characterization of the proteinaceous samples, after isolation from the SDS, was performed by capillary liquid chromatography (LC) with UV absorption detection and electrospay mass spectrometry (ESI-MS). Loading and clean-up of the samples and regeneration of the detergent trapping column were performed at 50 microl min(-1), resulting in sample clean-up times of only 30 s. SDS-containing tryptic digested protein samples were directly applied to the micro-precolumns without any previous sample pretreatment. The developed microcolumn switching method permits the on-line analysis of small tryptic digest samples by capillary LC/ESI-MS in the presence of SDS. The method is completely automated and can be performed unattended. The maximum amount of SDS, in terms of loadability and breakthrough, were determined. Also studied were the selection of the loading and clean-up solvents and the recovery of the peptides. Chromatographic separations and mass spectral data confirmed the removal of SDS.