Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization

A two-stage spin cartridge for integrated protein precipitation, digestion and SDS removal in a comparative bottom-up proteomics workflow

Protein precipitation with organic solvent is an effective means of depleting contaminants such as sodium dodecyl sulfate (SDS), while maintaining high analyte recovery. Here, we report the use of a disposable two-stage spin cartridge to facilitate isolation of the precipitated protein, with subsequent enzyme digestion and peptide cleanup in the cartridge. An upper filtration cartridge retains over 95% of the protein (10 μg BSA), with 99.75% detergent depleted from a sample initially containing 2% SDS. Following precipitation, a plug attached to the base of the filtration cartridge retains the solution to enable tryptic digestion in the vial, while a solid phase extraction cartridge attached to the base of the filter facilitates peptide cleanup post-digestion. A GELFrEE fractionated Escherichia coli proteome extract processed with the spin cartridge yields similar protein identifications compared to controls (226 vs 216 for control), and with an increased number of unique peptides (1753 vs 1554 for control). The device is applied to proteome characterization of rat kidneys experiencing a surgically induced ureteral tract obstruction, revealing several statistically altered proteins, consistent with the morphology and expected pathophysiology of the disease.

BIOLOGICAL SIGNIFICANCE

Conventionally, protein precipitation involves extended centrifugation to pellet the sample, with careful pipetting to remove the supernatant without disturbing the pellet. The method is not only time consuming but is highly subject to the skill of the individual, particularly at lower protein concentrations where the pellet may not be visible. As such, protein precipitation is often overlooked in proteomics, favoring column-based approaches to concentrate or purify samples. Here, all aspects of sample manipulation are integrated into a simple disposable cartridge. The device enables SDS depletion, sample preconcentration, resolubilization, derivatization, digestion, and peptide cleanup in a highly repeatable and easily multiplexed format. The device is ideally suited for comparative proteome studies. Antenatal hydronephrosis is a congenital disorder affecting 1-5% of all pregnancies, and can require surgical intervention to avoid loss of renal function. Using our device, we investigated the impact of hydronephrosis on the kidneys in a surgically induced animal model of the disease. Proteome analysis points to decreased metabolic activity in the obstructed kidney, with upregulation of proteins involved in cytoskeletal organization. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.

Multi-enzyme digestion FASP and the 'Total Protein Approach'-based absolute quantification of the Escherichia coli proteome

We describe a proteomic approach combining the multi-enzyme digestion FASP-sample processing strategy and the 'Total Protein Approach' applied to absolute quantification of proteins in Escherichia coli. Consecutive digestion of whole cell lysates with LysC and trypsin allowed the generation of two populations of peptides at a yield of 76%. Subsequent two 4-hour LC-MS/MS analyses allowed the identification of 19,000 unique peptides per sample. Notably, only 1.2 and 2.4% of the identified peptides were found to be incompletely cleaved by the LysC and trypsin, respectively. The analysis resulted in the identification of 2200 proteins per sample. We show high reproducibility of the approach, allowing the accurate estimation of cellular protein concentrations. Quantitative analysis of the DNA content per sample enabled the calculation of the protein content per bacterial cell and, as a result, estimation of protein copy numbers. The accuracy of these estimations was confirmed by analyzing protein complexes with known subunit stoichiometry and cellular abundances. In stationary culture, a single bacterium contains about 6500 copies of ribosomes, 300 molecules of RNA polymerase and 10 DNA polymerase assembles. The here presented experimental and computational workflow offers an easy way to analyze proteomes quantitatively.

BIOLOGICAL SIGNIFICANCE

We demonstrate a proteomic workflow for in-depth analysis of small proteomes with minimal fractionation extent and mass spectrometry measuring time. For the first time we provide the quantitative picture of the Escherichia coli proteome at protein copy number.

Urine sample preparation in 96-well filter plates for quantitative clinical proteomics

Urine is an important, noninvasively collected body fluid source for the diagnosis and prognosis of human diseases. Liquid chromatography mass spectrometry (LC-MS) based shotgun proteomics has evolved as a sensitive and informative technique to discover candidate disease biomarkers from urine specimens. Filter-aided sample preparation (FASP) generates peptide samples from protein mixtures of cell lysate or body fluid origin. Here, we describe a FASP method adapted to 96-well filter plates, named 96FASP. Soluble urine concentrates containing ~10 μg of total protein were processed by 96FASP and LC-MS resulting in 700-900 protein identifications at a 1% false discovery rate (FDR). The experimental repeatability, as assessed by label-free quantification and Pearson correlation analysis for shared proteins among replicates, was high (R ≥ 0.97). Application to urinary pellet lysates which is of particular interest in the context of urinary tract infection analysis was also demonstrated. On average, 1700 proteins (±398) were identified in five experiments. In a pilot study using 96FASP for analysis of eight soluble urine samples, we demonstrated that protein profiles of technical replicates invariably clustered; the protein profiles for distinct urine donors were very different from each other. Robust, highly parallel methods to generate peptide mixtures from urine and other body fluids are critical to increase cost-effectiveness in clinical proteomics projects. This 96FASP method has potential to become a gold standard for high-throughput quantitative clinical proteomics.

Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis

Despite recent developments in bottom-up proteomics, the need still exists in a fast, uncomplicated, and robust method for comprehensive sample processing especially when applied to low protein amounts. The suspension trapping method combines the advantage of efficient SDS-based protein extraction with rapid detergent removal, reactor-type protein digestion, and peptide cleanup. Proteins are solubilized in SDS. The sample is acidified and introduced into the suspension trapping tip incorporating the depth filter and hydrophobic compartments, filled with the neutral pH methanolic solution. The instantly formed fine protein suspension is trapped in the depth filter stack-this crucial step is aimed at separating the particulate matter in space. SDS and other contaminants are removed in the flow-through, and a protease is introduced. Following the digestion, the peptides are cleaned up using the tip's hydrophobic part. The methodology allows processing of protein loads down to the low microgram/submicrogram levels. The detergent removal takes about 5 min, whereas the tryptic proteolysis of a cellular lysate is complete in as little as 30 min. We have successfully utilized the method for analysis of cellular lysates, enriched membrane preparations, and immunoprecipitates. We expect that due to its robustness and simplicity, the method will become an essential proteomics tool.

Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture

Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and reliability of metaproteomic results. Specifically, the use of iterative searches and of suitable filters for taxonomic assignments is proposed with the aim of increasing coverage and trustworthiness of metaproteomic data.

Comparison of bottom-up proteomic approaches for LC-MS analysis of complex proteomes

Discovery-based proteomic studies aim to answer important biological questions by identifying as many proteins as possible. In order to accomplish this lofty goal, an effort must be placed on determining an optimal workflow that maximizes protein identifications. In this study, we compare protein extraction, digestion and fractionation methods for bottom-up proteomics using a human colon cancer cell line as our model system. Four different buffers for protein extraction, two digestion approaches, as well as three sample fractionation methods were evaluated in order to determine an accessible workflow that gives maximal protein identifications. Samples comparing these workflows were analyzed via UPLC paired with tandem MS on a Q-Exactive mass spectrometer. Our goal is to determine an optimal workflow to enable users to maximize protein identifications. Our results show that an increased number of confident protein identifications are attained with a filter-aided digestion approach as compared to an in-solution digestion. Overall SDS-PAGE fractionation leads to higher numbers of identifications than SCX SpinTip and reverse phased cartridge platforms. The novel aspect of this work is the comparison of two readily available, offline platforms for fractionation in reference to a traditional technique, SDS-PAGE.

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome

This work presents a comparative evaluation of several detergent-based sample preparation workflows for the MS-based analysis of bacterial proteomes, performed using the model organism Escherichia coli. Initially, RapiGest- and SDS-based buffers were compared for their protein extraction efficiency and quality of the MS data generated. As a result, SDS performed best in terms of total protein yields and overall number of MS identifications, mainly due to a higher efficiency in extracting high molecular weight (MW) and membrane proteins, while RapiGest led to an enrichment in periplasmic and fimbrial proteins. Then, SDS extracts underwent five different MS sample preparation workflows, including: detergent removal by spin columns followed by in-solution digestion (SC), protein precipitation followed by in-solution digestion in ammonium bicarbonate or urea buffer, filter-aided sample preparation (FASP), and 1DE separation followed by in-gel digestion. On the whole, about 1000 proteins were identified upon LC-MS/MS analysis of all preparations (>1100 with the SC workflow), with FASP producing more identified peptides and a higher mean sequence coverage. Each protocol exhibited specific behaviors in terms of MW, hydrophobicity, and subcellular localization distribution of the identified proteins; a comparative assessment of the different outputs is presented.