Ammonium dodecyl sulfate as an alternative to sodium dodecyl sulfate for protein sample preparation with improved performance in MALDI mass spectrometry

Differential Detergent Fractionation of Membrane Protein From Small Samples of Hepatocytes and Liver Tissue for Quantitative Proteomic Analysis of Drug Metabolizing Enzymes and Transporters

The fractionation of enough membrane protein from limited samples is challenging for MS-based quantitative targeted absolute proteomics (QTAP) of drug metabolizing enzymes (DMEs) and transporters. This study evaluated differential detergent fractionation (DDF) of membrane protein from progressively smaller numbers of primary mouse hepatocytes (5 million down to 50,000 cells) and limited liver tissue (25-50 mg) in quantifying select DMEs and transporters by QTAP. Two non-ionic detergents, digitonin and Triton-X-100, were applied in sequence to permeabilize cells and extract membrane proteins. Comparison was made with a membrane protein extraction kit and with homogenization in hypotonic buffer and subsequent differential centrifugation (DC). DDF produced linear membrane protein yields with increasing hepatocyte numbers and better permeabilization evidenced by the higher ratio of cytosolic to membrane protein yields. DDF produced 5-times more membrane protein from liver tissue than DC. The concentration of DMEs and transporters remained consistent in the fractions prepared by DDF from progressively smaller numbers of hepatocytes, but declined in kit fractions. In liver tissue, the concentrations were comparatively higher in DDF versus kit and DC. In conclusion, sequential digitonin and Triton-X-100 fractionation of membrane protein from limited samples is efficient, reproducible and cost-effective for QTAP of DMEs and transporters.

Enhancing Membrane Protein Identification Using a Simplified Centrifugation and Detergent-Based Membrane Extraction Approach

Membrane proteins may act as transporters, receptors, enzymes, and adhesion-anchors, accounting for nearly 70% of pharmaceutical drug targets. Difficulties in efficient enrichment, extraction, and solubilization still exist because of their relatively low abundance and poor solubility. A simplified membrane protein extraction approach with advantages of user-friendly sample processing procedures, good repeatability and significant effectiveness was developed in the current research for enhancing enrichment and identification of membrane proteins. This approach combining centrifugation and detergent along with LC-MS/MS successfully identified higher proportion of membrane proteins, integral proteins and transmembrane proteins in membrane fraction (76.6%, 48.1%, and 40.6%) than in total cell lysate (41.6%, 16.4%, and 13.5%), respectively. Moreover, our method tended to capture membrane proteins with high degree of hydrophobicity and number of transmembrane domains as 486 out of 2106 (23.0%) had GRAVY > 0 in membrane fraction, 488 out of 2106 (23.1%) had TMs ≥ 2. It also provided for improved identification of membrane proteins as more than 60.6% of the commonly identified membrane proteins in two cell samples were better identified in membrane fraction with higher sequence coverage. Data are available via ProteomeXchange with identifier PXD008456.

Ionic liquids as buffer additives in ionic liquid-polyacrylamide gel electrophoresis separation of mixtures of low and high molecular weight proteins

Three novel ionic liquids (ILs) [C_nPBr] (n= 4, 6, 8) have been synthesized and were used as buffer additives in IL-PAGE separation of mixture of acidic proteins.

Perfluorooctanoic acid and ammonium perfluorooctanoate: volatile surfactants for proteome analysis?

RATIONALE

Fluorinated surfactants are being explored as mass spectrometry (MS)-friendly alternatives to sodium dodecyl sulfate (SDS) for proteome analysis. Previous work demonstrates perfluorooctanoic acid (PFOA) to be compatible with electrospray ionization (ESI)-MS. The high volatility of PFOA provides an intrinsic approach to potentially eliminate the surfactant during ESI, or alternatively through solvent evaporation prior to MS. The ammonium salt of PFOA, ammonium perfluorooctanoate (APFO), is likely favored for proteome experiments; the MS and liquid chromatography (LC)/MS tolerance of APFO has not been established for proteome applications.

METHODS

Standard proteins and peptides, as well as a yeast proteome mixture, were individually spiked with surfactants (APFO, PFOA, SDS), and subjected to direct infusion ESI-MS, LC/MS/MS and LC/UV. The level of fluorinated surfactant remaining after solvent evaporation under varying conditions (time, pH, salt and protein content) was quantified and compared to the threshold tolerance level of the surfactant in an MS experiment (determined herein).

RESULTS

Whereas PFOA is found ineffective at assisting protein solubilization, APFO is as effective as SDS for resolubilization of acetone-precipitated yeast proteins (~100% recovery). Unfortunately, the LC and MS threshold tolerance of APFO is only minimally greater than SDS (~2-fold higher concentration to cause 50% suppression). Nonetheless, the benefits of APFO in a proteome experiment are realized following a one-step evaporation protocol for removal of the surfactant in acidified solvent.

CONCLUSIONS

APFO is considered a favoured alternative to SDS for proteome solubilization. Strictly speaking, APFO is not an 'MS-friendly' surfactant for proteome characterization; the detergent not only suppresses ESI signals at high concentration, but also perturbs reversed phase separation. However, the simplicity of APFO removal ahead of LC/MS justifies its use over the conventional SDS.

Phosphopeptide analysis by directly coupling two-dimensional planar electrochromatography/thin-layer chromatography with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A novel strategy is presented for the fractionation of complex peptide mixtures using two-dimensional planar electrochromatography/thin-layer chromatography (2D PEC/TLC). Phosphopeptides migrate more slowly in the first dimension, based upon their anionic phosphate residues, and certain predominantly acidic phosphopeptides even migrate in the opposite direction, relative to the bulk of the peptides. Phosphopeptides are further distinguished based upon hydrophilicity in the second dimension. This permits a restricted region of the plate to be directly interrogated for the presence of phosphopeptides by mass spectrometry (MS). Phosphopeptide analysis from the plates by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-MS and tandem MS enabled peptide sequencing and identification.

Three-layer matrix/sample preparation method for MALDI MS analysis of low nanomolar protein samples

A robust and sensitive sample preparation method is presented for matrix-assisted laser desorption ionization (MALDI) mass spectrometric analysis of low nanomolar concentrations of proteins containing high amounts of common salts and buffers. This method involves the production of densely packed sub-micrometer matrix crystals by depositing a matrix solution on top of a matrix seed-layer prepared on a MALDI target. A sub-microliter aliquot of analyte solution is then directly added to the top of the matrix crystals to form a thin-layer. alpha-Cyano-4-hydroxycinnamic acid (4-HCCA) is used as matrix and demonstrated to give better performance than other commonly used matrices, such as 2,5-dihydroxybenzoic acid (DHB), 2-(4-hydroxy-phenylazo) benzoic acid (HABA), or sinapinic acid. This three-layer method is shown to be superior to the other MALDI sample preparation methods, particularly for handling low nanomolar protein solutions containing salts and buffers.

A targeted proteomic approach for the analysis of rat liver mitochondrial outer membrane proteins with extensive sequence coverage

Membrane proteins play an important role in cellular function. However, their analysis by mass spectrometry often is hindered by their hydrophobicity and/or low abundance. In this article, we present a method for the mass spectrometric analysis of membrane proteins based on the isolation of the resident membranes, isolation of the proteins by gel electrophoresis, and electroelution followed by enzymatic digestion by both trypsin and proteinase K. With this method, we have achieved 82-99% sequence coverage for the membrane proteins carnitine palmitoyltransferase-I (CPT-I), long-chain acyl-CoA synthetase (LCAS), and voltage-dependent anion channel (VDAC), isolated from rat liver mitochondrial outer membranes, including the transmembrane domains of these integral membrane proteins. This high sequence coverage allowed the identification of the isoforms of the proteins under study. This methodology provides a targeted approach for examining membrane proteins in detail.

Improved analysis of membrane protein by PVDF-aided, matrix-assisted laser desorption/ionization mass spectrometry

Characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. This study presents the utility of the polyvinylidene difluoride (PVDF) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The hydrophobic adsorption of protein, particularly membrane proteins, on the PVDF surface enables efficient on-PVDF washing to remove high concentrations of detergents and salts, such as up to 5% sodium dodecyl sulfate (SDS). The enhanced spectrum quality for MALDI detection is particularly notable for high molecular weight proteins. By using on-PVDF washing prior to MALDI detection, we obtained protein profiles of the detergent-containing and detergent-insoluble membrane fractions from Methylococcus capsulatus (Bath). Similar improvements of signal-to-noise ratios were shown on the MALDI spectra for proteins electroblotted from SDS-polyacrylamide gel electrophoresis (SDS-PAGE) onto the PVDF membrane. We have applied this strategy to obtain intact molecular weights of the particulate methane monooxygenase (pMMO) composed of three intrinsic membrane-bound proteins, PmoA, PmoB, and PmoC. Together with peptide sequencing by tandem mass spectrometry, post-translational modifications including N-terminal acetylation of PmoA and PmoC and alternative C-terminal truncation of PmoB were identified. The above results show that PVDF-aided MALDI-MS can be an effective approach for profiling and characterization of membrane proteins.

Nonacid cleavable detergents applied to MALDI mass spectrometry profiling of whole cells

Although cleavable detergents were first synthesized a number of years ago, they have only recently been successfully applied to problems involving biological molecules. Recent reports have demonstrated that these compounds are useful for applications involving both 2D PAGE and mass spectrometry. However, most cleavable surfactants have utilized acid-labile functional groups to affect cleavage. In applications where extreme pH is required, acid cleavable detergents have limited usefulness. We report the synthesis of fluoride cleavable silane compounds and photolabile cinnamate esters as cleavable detergents having alternative cleavage chemistries than previously reported cleavable detergents. These compounds were applied to whole cell analysis using MALDI mass spectrometry, and it was demonstrated that their use results in an increase in the number of proteins analyzed by increasing protein solubility.

Interactions between sodium dodecyl sulfate micelles and peptides during matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of proteolytic digests

Although sodium dodecyl sulfate (SDS) is routinely used as a denaturing agent for proteins, its presence is highly detrimental on the analysis of peptides and proteins by mass spectrometry. It has been found, however, that when SDS is present in concentrations near to or above its critical micelle concentration (CMC), improvements in the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of peptide mixtures or hydrophobic proteins are obtained. To elucidate possible explanations for such improvements, here we have undertaken a study examining the effect of SDS micelles on peptide mixtures. Fluorescently labeled peptides were used as probes to determine whether hydrophobic or hydrophilic peptides interact exclusively with SDS micelles. In addition, four globular proteins were digested with trypsin and then various amounts of SDS were added before MALDI mass spectrometry. To examine the role of mixture complexity on the mass spectral results, the tryptic digest of bovine serum albumin was also fractionated according to hydrophobicity before SDS treatment. Results from these experiments suggest that micelle-peptide interactions increase peptide-matrix cocrystallization irrespective of analyte hydrophobicity. As these studies were performed using the dried-droplet method of sample spotting, the presence of micelles is also hypothesized to reduce Marangoni effects during the crystallization process.

Relative binding strength of terpyridine model complexes under matrix-assisted laser desorption/ionization mass spectrometry conditions

The relative binding strength of a series of terpyridine metal complexes of the type [M(II)L(2)](+) was investigated by using variable laser intensities in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). A model terpyridine ligand, 4'-(1,4,7-trioxa-octyl)-2,2':6',2"-terpyridine, was prepared and complexed with a series of transition metal ions including cadmium, cobalt, copper, iron, manganese, nickel and ruthenium. The relative binding strength of these complexes can be obtained by measuring MALDI mass spectra of the prepared compounds at different laser intensities. The ratio of the signal intensities belonging to the ligand [LH](+) and the complex [ML(2)](+) ([LH](+) /[ML(2)](+)) depends on the laser intensity utilized for the spectrum acquisition. By considering an [LH](+)/[ML(2)](+) ratio > 10 as the point of complete complex dissociation, it is possible to establish a row of complex stabilities depending on the kind of metal ion.