Increases in Global and East Asian Nitrogen Trifluoride (NF3) Emissions Inferred from Atmospheric Observations.

Nitrogen trifluoride (NF3) is a potent and long-lived greenhouse gas that is widely used in the manufacture of semiconductors, photovoltaic cells, and flat panel displays. Using atmospheric observations from eight monitoring stations from the Advanced Global Atmospheric Gases Experiment (AGAGE) and inverse modeling with a global 3-D atmospheric chemical transport model (GEOS-Chem), we quantify global and regional NF3 emission from 2015 to 2021. We find that global emissions have grown from 1.93 ± 0.58 Gg yr-1 (± one standard deviation) in 2015 to 3.38 ± 0.61 Gg yr-1 in 2021, with an average annual increase of 10% yr-1. The available observations allow us to attribute significant emissions to China (0.93 ± 0.15 Gg yr-1 in 2015 and 1.53 ± 0.20 Gg yr-1 in 2021) and South Korea (0.38 ± 0.07 Gg yr-1 to 0.65 ± 0.10 Gg yr-1). East Asia contributes around 73% of the global NF3 emission increase from 2015 to 2021: approximately 41% of the increase is from emissions from China (with Taiwan included), 19% from South Korea, and 13% from Japan. For Japan, which is the only one of these three countries to submit annual NF3 emissions to UNFCCC, our bottom-up and top-down estimates are higher than reported. With increasing demand for electronics, especially flat panel displays, emissions are expected to further increase in the future.

Rising Perfluorocyclobutane (PFC-318, c-C4F8) Emissions in China from 2011 to 2020 Inferred from Atmospheric Observations.

Global atmospheric emissions of perfluorocyclobutane (c-C4F8, PFC-318), a potent greenhouse gas, have increased rapidly in recent years. Combining atmospheric observations made at nine Chinese sites with a Lagrangian dispersion model-based Bayesian inversion technique, we show that PFC-318 emissions in China grew by approximately 70% from 2011 to 2020, rising from 0.65 (0.54-0.72) Gg year-1 in 2011 to 1.12 (1.05-1.19) Gg year-1 in 2020. The PFC-318 emission increase from China played a substantial role in the overall increase in global emissions during the study period, contributing 58% to the global total emission increase. This growth predominantly originated in eastern China. The regions with high emissions of PFC-318 in China overlap with areas densely populated with polytetrafluoroethylene (PTFE) factories, implying that fluoropolymer factories are important sources of PFC-318 emissions in China. Our investigation reveals an emission factor of approximately 3.02 g of byproduct PFC-318 emissions per kg of hydrochlorofluorocarbon-22 (HCFC-22) feedstock use in the production of tetrafluoroethylene (TFE) (for PTFE production) and hexafluoropropylene (HFP) if we assume all HCFC-22 produced for feedstock uses in China are pyrolyzed to produce PTFE and HFP. Further facility-level sampling and analysis are needed for a more precise evaluation of emissions from these factories.

First Atmospheric Measurements and Emission Estimates of HFO-1336mzz(Z).

For the past few years, short-lived unsaturated halocarbons have been marketed as environmentally friendly replacements for long-lived halogenated greenhouse gases and ozone-depleting substances. The phase-in of unsaturated halocarbons for various applications, such as refrigeration and foam blowing, can be tracked by their emergence and increase in the atmosphere. We present the first atmospheric measurements of the hydrofluoroolefin (HFO) HFO-1336mzz(Z) ((Z)-1,1,1,4,4,4-hexafluoro-2-butene, cis-CF3CH═CHCF3), a newly used unsaturated hydrofluorocarbon. HFO-1336mzz(Z) has been detected in >90% of all measurements since 2018 during multi-month campaigns at three Swiss and one Dutch location. Since 2019, it is found in ∼30% of all measurements that run continuously at the Swiss high-altitude Jungfraujoch station. During pollution events, mole fractions of up to ∼10 ppt were observed. Based on our measurements, Swiss and Dutch emissions were estimated at 2-7 Mg yr-1 (2019-2021) and 30 Mg yr-1 (2022), respectively. Modeled spatial emission distributions only partly conform to population density in both countries. Monitoring the presence of new unsaturated halocarbons in the atmosphere is crucial since long-term effects of their degradation products are still debated. Furthermore, the production of HFOs involves climate-active substances, which may leak to the atmosphere─in the case of HFO-1336mzz(Z), for example, the ozone-depleting CFC-113a (CF3CCl3).

Automated fragment formula annotation for electron ionisation, high resolution mass spectrometry: application to atmospheric measurements of halocarbons.

BACKGROUND: Non-target screening consists in searching a sample for all present substances, suspected or unknown, with very little prior knowledge about the sample. This approach has been introduced more than a decade ago in the field of water analysis, together with dedicated compound identification tools, but is still very scarce for indoor and atmospheric trace gas measurements, despite the clear need for a better understanding of the atmospheric trace gas composition. For a systematic detection of emerging trace gases in the atmosphere, a new and powerful analytical method is gas chromatography (GC) of preconcentrated samples, followed by electron ionisation, high resolution mass spectrometry (EI-HRMS). In this work, we present data analysis tools to enable automated fragment formula annotation for unknown compounds measured by GC-EI-HRMS. RESULTS: Based on co-eluting mass/charge fragments, we developed an innovative data analysis method to reliably reconstruct the chemical formulae of the fragments, using efficient combinatorics and graph theory. The method does not require the presence of the molecular ion, which is absent in [Formula: see text]40% of EI spectra. Our method has been trained and validated on >50 halocarbons and hydrocarbons, with 3-20 atoms and molar masses of 30-330 g mol[Formula: see text], measured with a mass resolution of approx. 3500. For >90% of the compounds, more than 90% of the annotated fragment formulae are correct. Cases of wrong identification can be attributed to the scarcity of detected fragments per compound or the lack of isotopic constraint (no minor isotopocule detected). CONCLUSIONS: Our method enables to reconstruct most probable chemical formulae independently from spectral databases. Therefore, it demonstrates the suitability of EI-HRMS data for non-target analysis and paves the way for the identification of substances for which no EI mass spectrum is registered in databases. We illustrate the performances of our method for atmospheric trace gases and suggest that it may be well suited for many other types of samples. The L-GPL licenced Python code is released under the name ALPINAC for ALgorithmic Process for Identification of Non-targeted Atmospheric Compounds.

Unexpected nascent atmospheric emissions of three ozone-depleting hydrochlorofluorocarbons.

Global and regional atmospheric measurements and modeling can play key roles in discovering and quantifying unexpected nascent emissions of environmentally important substances. We focus here on three hydrochlorofluorocarbons (HCFCs) that are restricted by the Montreal Protocol because of their roles in stratospheric ozone depletion. Based on measurements of archived air samples and on in situ measurements at stations of the Advanced Global Atmospheric Gases Experiment (AGAGE) network, we report global abundances, trends, and regional enhancements for HCFC-132b ([Formula: see text]), which is newly discovered in the atmosphere, and updated results for HCFC-133a ([Formula: see text]) and HCFC-31 ([Formula: see text]ClF). No purposeful end-use is known for any of these compounds. We find that HCFC-132b appeared in the atmosphere 20 y ago and that its global emissions increased to 1.1 Gg⋅y-1 by 2019. Regional top-down emission estimates for East Asia, based on high-frequency measurements for 2016-2019, account for ∼95% of the global HCFC-132b emissions and for ∼80% of the global HCFC-133a emissions of 2.3 Gg⋅y-1 during this period. Global emissions of HCFC-31 for the same period are 0.71 Gg⋅y-1 Small European emissions of HCFC-132b and HCFC-133a, found in southeastern France, ceased in early 2017 when a fluorocarbon production facility in that area closed. Although unreported emissive end-uses cannot be ruled out, all three compounds are most likely emitted as intermediate by-products in chemical production pathways. Identification of harmful emissions to the atmosphere at an early stage can guide the effective development of global and regional environmental policy.

Long-term Observations of Atmospheric Halogenated Organic Trace Gases.

CFCs (chlorofluorocarbons) and other strong ozone-depleting halogenated organic trace gases were used in numerous industrial, household and agriculture applications. First atmospheric measurements of CFCs were performed in the 1970s, well ahead of the detection of the ozone hole in the 1980s. The continuous observation of these ozone-depleting substances (ODSs) is crucial for monitoring their global ban within the Montreal Protocol. In addition, also HFCs (fluorinated hydrocarbons) are measured, which were introduced as substitutes of ODSs and are potent greenhouse gases. Since 2000, Empa continuously measures more than 50 halogenated trace gases at the high-Alpine station of Jungfraujoch (3850 m asl) as part of the global AGAGE network (Advanced Global Atmospheric Gases Experiment). Jungfraujoch is the highest location worldwide where such measurements are performed, and the site where several of these compounds were measured in the atmosphere for the first time. The measurements at Jungfraujoch and at other globally well-positioned sites serve as an early warning system, i. e. before potentially harmful halogenated organic substances can accumulate and detrimentally affect the natural environment.

Recent Trends in Stratospheric Chlorine From Very Short-Lived Substances.

Very short-lived substances (VSLS), including dichloromethane (CH2Cl2), chloroform (CHCl3), perchloroethylene (C2Cl4), and 1,2-dichloroethane (C2H4Cl2), are a stratospheric chlorine source and therefore contribute to ozone depletion. We quantify stratospheric chlorine trends from these VSLS (VSLCltot) using a chemical transport model and atmospheric measurements, including novel high-altitude aircraft data from the NASA VIRGAS (2015) and POSIDON (2016) missions. We estimate VSLCltot increased from 69 (±14) parts per trillion (ppt) Cl in 2000 to 111 (±22) ppt Cl in 2017, with >80% delivered to the stratosphere through source gas injection, and the remainder from product gases. The modeled evolution of chlorine source gas injection agrees well with historical aircraft data, which corroborate reported surface CH2Cl2 increases since the mid-2000s. The relative contribution of VSLS to total stratospheric chlorine increased from ~2% in 2000 to ~3.4% in 2017, reflecting both VSLS growth and decreases in long-lived halocarbons. We derive a mean VSLCltot growth rate of 3.8 (±0.3) ppt Cl/year between 2004 and 2017, though year-to-year growth rates are variable and were small or negative in the period 2015-2017. Whether this is a transient effect, or longer-term stabilization, requires monitoring. In the upper stratosphere, the modeled rate of HCl decline (2004-2017) is -5.2% per decade with VSLS included, in good agreement to ACE satellite data (-4.8% per decade), and 15% slower than a model simulation without VSLS. Thus, VSLS have offset a portion of stratospheric chlorine reductions since the mid-2000s.

Reconciling reported and unreported HFC emissions with atmospheric observations.

We infer global and regional emissions of five of the most abundant hydrofluorocarbons (HFCs) using atmospheric measurements from the Advanced Global Atmospheric Gases Experiment and the National Institute for Environmental Studies, Japan, networks. We find that the total CO2-equivalent emissions of the five HFCs from countries that are required to provide detailed, annual reports to the United Nations Framework Convention on Climate Change (UNFCCC) increased from 198 (175-221) Tg-CO2-eq ⋅ y(-1) in 2007 to 275 (246-304) Tg-CO2-eq ⋅ y(-1) in 2012. These global warming potential-weighted aggregated emissions agree well with those reported to the UNFCCC throughout this period and indicate that the gap between reported emissions and global HFC emissions derived from atmospheric trends is almost entirely due to emissions from nonreporting countries. However, our measurement-based estimates of individual HFC species suggest that emissions, from reporting countries, of the most abundant HFC, HFC-134a, were only 79% (63-95%) of the UNFCCC inventory total, while other HFC emissions were significantly greater than the reported values. These results suggest that there are inaccuracies in the reporting methods for individual HFCs, which appear to cancel when aggregated together.

First observations of the fourth generation synthetic halocarbons HFC-1234yf, HFC-1234ze(E), and HCFC-1233zd(E) in the atmosphere.

Halogenated alkenes are a class of anthropogenic substances, which replace ozone-depleting substances and long-lived greenhouse gases in the foam-blowing, refrigeration, and solvent sectors. We report the first multiyear atmospheric measurements of the hydrofluorocarbons HFC-1234yf (2,3,3,3-tetrafluoroprop-1-ene, CF3CF═CH2), and HFC-1234ze(E) (E-1,3,3,3-tetrafluoroprop-1-ene trans-CF3CH═CHF), and the hydrochlorofluorocarbon HCFC-1233zd(E) (E-1-chloro-3,3,3-trifluoroprop-1-ene trans-CF3CH═CHCl) from the high altitude observatory at Jungfraujoch and from urban Dubendorf (Switzerland). When observations started in 2011 HFC-1234yf was undetectable at Jungfraujoch (mole fractions <0.003 ppt, parts-per-trillion, 10(-12)) but since then the percentage of measurements with detectable mole fractions has steadily increased to 4.5% in 2014. By contrast, in 2014 HFC-1234ze(E) was detectable in half of our samples at Jungfraujoch and in all samples at Dubendorf demonstrating the wide use of this compound within the air mass footprints of the stations. Our back trajectory analysis for the Jungfraujoch observations suggests high emission strength of HFC-1234ze(E) in the Belgium/Netherlands region. HCFC-1233zd(E) is present at very low mole fractions (typically <0.03 ppt) at both stations, and features pronounced seasonality and a general absence of pollution events during our 2013-2014 measurements. This is indicative of the presence of significant emissions from source locations outside the footprints of the two stations. Based on a simple one-box model calculation we estimate globally increasing HCFC-1233zd(E) emissions from 0.2 Gg yr(-1) in 2013 to 0.5 Gg yr(-1) for 2014.

Comparison of halocarbon measurements in an atmospheric dry whole air sample.

The growing awareness of climate change/global warming, and continuing concerns regarding stratospheric ozone depletion, will require continued measurements and standards for many compounds, in particular halocarbons that are linked to these issues. In order to track atmospheric mole fractions and assess the impact of policy on emission rates, it is necessary to demonstrate measurement equivalence at the highest levels of accuracy for assigned values of standards. Precise measurements of these species aid in determining small changes in their atmospheric abundance. A common source of standards/scales and/or well-documented agreement of different scales used to calibrate the measurement instrumentation are key to understanding many sets of data reported by researchers. This report describes the results of a comparison study among National Metrology Institutes and atmospheric research laboratories for the chlorofluorocarbons (CFCs) dichlorodifluoromethane (CFC-12), trichlorofluoromethane (CFC-11), and 1,1,2-trichlorotrifluoroethane (CFC-113); the hydrochlorofluorocarbons (HCFCs) chlorodifluoromethane (HCFC-22) and 1-chloro-1,1-difluoroethane (HCFC-142b); and the hydrofluorocarbon (HFC) 1,1,1,2-tetrafluoroethane (HFC-134a), all in a dried whole air sample. The objective of this study is to compare calibration standards/scales and the measurement capabilities of the participants for these halocarbons at trace atmospheric levels. The results of this study show agreement among four independent calibration scales to better than 2.5% in almost all cases, with many of the reported agreements being better than 1.0%.

European emissions of halogenated greenhouse gases inferred from atmospheric measurements.

European emissions of nine representative halocarbons (CFC-11, CFC-12, Halon 1211, HCFC-141b, HCFC-142b, HCFC-22, HFC-125, HFC-134a, HFC-152a) are derived for the year 2009 by combining long-term observations in Switzerland, Italy, and Ireland with campaign measurements from Hungary. For the first time, halocarbon emissions over Eastern Europe are assessed by top-down methods, and these results are compared to Western European emissions. The employed inversion method builds on least-squares optimization linking atmospheric observations with calculations from the Lagrangian particle dispersion model FLEXPART. The aggregated halocarbon emissions over the study area are estimated at 125 (106-150) Tg of CO(2) equiv/y, of which the hydrofluorocarbons (HFCs) make up the most important fraction with 41% (31-52%). We find that chlorofluorocarbon (CFC) emissions from banks are still significant and account for 35% (27-43%) of total halocarbon emissions in Europe. The regional differences in per capita emissions are only small for the HFCs, while emissions of CFCs and hydrochlorofluorocarbons (HCFCs) tend to be higher in Western Europe compared to Eastern Europe. In total, the inferred per capita emissions are similar to estimates for China, but 3.5 (2.3-4.5) times lower than for the United States. Our study demonstrates the large benefits of adding a strategically well placed measurement site to the existing European observation network of halocarbons, as it extends the coverage of the inversion domain toward Eastern Europe and helps to better constrain the emissions over Central Europe.

Performance of HPLC/MS microchips in isocratic and gradient elution modes.

We analyzed the chromatographic performance of particle-packed, all-polyimide high-performance liquid chromatography/mass spectrometry (HPLC/MS) microchips in terms of their hydraulic permeabilities and separation efficiency under isocratic and gradient elution conditions. The separation channels of the chips (with ca 50 microm x 75 microm trapezoidal cross-section and a length of 43 mm) were slurry packed with either 3.5 or 5 microm spherical porous C18-silica particles. A custom-built holder enveloped the chip during packing to prevent channel deformation and delamination from high pressures. It is shown that the packing conditions significantly impact the packing density of the HPLC/MS chips, which determines their performance in both, isocratic and gradient elution modes. Even with steep solvent gradients, peak shape and chromatographic resolution for the densely packed HPLC/MS chips are much improved. Our data show that the analytical power of the HPLC/MS chip is limited by the quality of the chromatographic separation.

A fluorescent derivatization method of proteins for the detection of low-level impurities by microchip capillary gel electrophoresis.

A novel pre-chip fluorescent derivatization method is presented for protein sizing and quantification by microchip CGE. The derivatization reaction employed a water-soluble and stable fluorescent dye and was performed under conditions that favored the formation of homogeneous reaction products. The method delivered in terms of protein sizing similar results as microchip CGE with on-chip staining but showed an extended linear dynamic range for protein quantification encompassing four orders of magnitude. The sensitivity of the method was similar to standard silver-stained planar gels. The characterization of derivatization reaction products by MS and preparative isoelectric focusing indicated that a constant degree of dye molecule tagging was obtained over a broad range of protein/dye ratios. The method allowed detecting and quantifying an impurity spiked into an antibody preparation down to a level of 0.05%. Advantages of this method compared with CGE approaches with pre-column derivatization include a shorter analysis time and an increased robustness and ease of use.

HPLC-Chip/MS technology in proteomic profiling.

HPLC-chip/MS is a novel nanoflow analytical technology conducted on a microfabricated chip that allows for highly efficient HPLC separation and superior sensitive MS detection of complex proteomic mixtures. This is possible through on-chip preconcentration and separation with fluidic connection made automatically in a leak-tight fashion. Minimum precolumn and postcolumn peak dispersion and uncompromised ease of use result in compounds eluting in bands of only a few nanoliters. The chip is fabricated out of bio-inert polyimide-containing channels and integrated chip structures, such as an electrospray emitter, columns, and frits manufactured by laser ablation technology. Meanwhile, a variety of HPLC-chips differing in design and stationary phase are commercially available, which provide a comprehensive solution for applications in proteomics, glycomics, biomarker, and pharmaceutical discovery. The HPLC-chip can also be easily integrated into a multidimensional separation workflow where different orthogonal separation techniques are combined to solve a highly complex separation problems. In this chapter, we describe in detail the methodological chip usage and functionality and its application in the elucidation of the protein profile of human nucleoli.

Assessing a novel microfluidic interface for shotgun proteome analyses.

Microfluidic interfaces coupled to ESI mass spectrometers hold great potential for proteomics as they have been shown to augment the overall sensitivity of measurements and require only a minimum of operator manipulations as compared to conventional nano-LC interfaces. Here, we evaluated a new type of HPLC-Chips holding larger enrichment columns (thus an increased sample loading capacity) for gel-free proteome studies. A tryptic digest of a human T-cell proteome was fractionated by strong cation exchange chromatography and selected fractions were analyzed by MS/MS on an IT mass spectrometer using both the new HPLC-Chip as well as a conventional nano-LC-MS/MS interface. Our results indicate that the HPLC-Chip is capable of handling very complex peptide mixtures and, in fact, leads to the identification of more peptides and proteins as compared to when a conventional interface was used. The HPLC-Chip preferentially produced doubly charged tryptic peptides. We further show that MS/MS spectra of doubly charged tryptic peptide ions are more readily identified by MASCOT as compared to those from triply charged precursors and thus argue that besides the improved chromatographic conditions provided by the HPLC-Chip, its peptide charging profile might be a secondary factor leading to an increased proteome coverage.

European emissions of HFC-365mfc, a chlorine-free substitute for the foam blowing agents HCFC-141b and CFC-11.

HFC-365mfc (1,1,1,3,3-pentafluorobutane) is an industrial chemical used for polyurethane foam blowing. From early 2003, HFC-365mfc has been commercially produced as a substitute for HCFC-141b, whose use in Europe has been banned since January 2004. We describe the first detection of HFC-365mfc in the atmosphere and report on a 2 year long record at the high Alpine station of Jungfraujoch (Switzerland) and the Atlantic coast station of Mace Head (Ireland). The measurements at Jungfraujoch are used to estimate the central European emissions of HFC-365mfc, HCFC-141b, and CFC-11. For HFC-365mfc, we estimate the central European emissions (Germany, France, Italy, Switzerland, The Netherlands, Belgium, and Luxembourg) in 2003 and 2004 as 400-500 tonnes year(-1). These emissions are about one-third lower on a per capita basis than what we estimate from the Mace Head measurements for the total of Europe. The estimated emissions of HCFC-141b for central Europe are higher (i.e., 7.2-3.5 ktonnes year(-1)) with a decreasing trend in the period from 2000 to 2004. Residual emissions of CFC-11 are estimated at 2.4-4.7 ktonnes year(-1) in the same time period. The Po Valley (northern Italy) appears to be a main source region for HFC-365mfc and for the former blowing agents HCFC-141b and CFC-11. In 2004, the emissions of HFC-365mfc arose from a wider region of Europe, which we attribute to an increased penetration of HFC-365mfc into the European market.

Multi-dimensional HPLC/MS of the nucleolar proteome using HPLC-chip/MS.

The proteome of the human nucleolus was investigated in a single analysis using off-line strong cation exchange chromatography and microfraction collection combined with HPLC-chip/MS. The analysis was conducted either as a 1-D workflow with HPLC-chip alone or as a 2-D workflow. Two hundred and six unique proteins were identified in the International Protein Index human database corresponding to 2024 unique tryptic peptides identified in the 2-D analysis. In contrast, only 34 proteins and 151 corresponding tryptic peptides were found by applying a 1-D separation strategy. This clearly indicated that the complexity of the samples required the combination of more than one orthogonal separation technique. Stringent database search criteria, including reversal of sequences and therefore better exclusion of false-positive identifications, were applied for reliable protein identification.

LC-nanospray-MS/MS analysis of hydrophobic proteins from membrane protein complexes isolated by blue-native electrophoresis.

The application of two-dimensional electrophoresis for the identification of hydrophobic membrane proteins is principally hampered by precipitation of many of these proteins during first-dimension, isoelectric focusing. Therefore new strategies towards the identification and characterization of membrane proteins are being developed. In this work we present a direct and rapid approach from blue-native gels to mass spectrometry, which allows the analyses of complete complexes and prevents protein aggregation of hydrophobic regions during electrophoresis. We combine blue-native gel electrophoresis and liquid chromatography--nanospray-iontrap tandem mass spectrometry to analyze the composition of oxidative phosphorylation complexes I, III, IV and V from bovine-heart mitochondria as a model system containing a number of highly hydrophobic proteins. Bands from blue-native gels were subjected either to in-gel or to in-solution tryptic digestion. The obtained peptide mixtures were further analyzed by liquid chromatography--tandem mass spectrometry and the corresponding proteins were identified by database search. From a total of 86 proteins, 67 protein subunits could be identified including all highly hydrophobic components, except the ND4L and ND6 subunits of complex I. We demonstrate that liquid chromatography--tandem mass spectrometry combined to blue-native electrophoresis is a straightforward tool for proteomic analysis of multiprotein complexes, and especially for the identification of very hydrophobic membrane protein constituents that are not accessible by common isoelectric focusing/sodium dodecyl sulphate gel electrophoresis.

Coupling of nanoflow liquid chromatography to matrix-assisted laser desorption/ionization mass spectrometry: real-time liquid chromatography run mapping on a MALDI plate.

The major obstacle in the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) instruments in the analysis of complex proteome samples is the lack of a direct coupling of a highly resolving separation technique with the mass spectrometer itself. To overcome this drawback, a spotting device for capillary and nanoflow liquid chromatography (LC) with a special liquid deposition principle for lowest volumes was developed. The instrument is able to perform MALDI spotting in real time in order to deposit the LC run on the MALDI plate, and therefore couples the high resolution power of nano-RP-HPLC separation directly with MALDI-MS. This work describes the development and optimization of a method for spotting with online matrix addition, and illustrates its use in the analysis of a complex proteome sample.

Optimization of two-dimensional off-line LC/MS separations to improve resolution of complex proteomic samples.

In off-line 2D-HPLC a continuous salt gradient is applied in the first separation dimension. This increases the number of identified proteins from complex samples significantly due to higher chromatographic resolution compared to stepwise elution. Achievement of optimal resolution requires the optimization of the two separation dimensions. The influence of LC elution gradients in the first and second dimensions, of analysis time, of stationary-phase material, and of column dimensions was systematically investigated in order to obtain information on the overall peak capacity of the separation system. Provided data indicate that for complex samples such as an E. coli cell extract, a shallow LC SCX gradient with a high number of collected fractions significantly increases the overall peak capacity while for lower complexity samples short gradients with few fractions were sufficient to obtain a maximum of identified peptides. In addition, column dimensions and materials exhibited a strong effect on the overall efficiency of the 2D HPLC separation. The outcome of these experiments could hence serve as a guideline for investigators to adapt their method for the separation of their specific proteome sample to achieve a maximum of peptide sequence information by 2D LC MS/MS analysis.