A method to enhance a1 ions and application for peptide sequencing and protein identification

A simplified sample preparation for hair and skin proteins towards the application of archaeological fur and leather

Conventional protocols for proteomics analysis usually start by extracting or solubilizing the proteins from their substrates. This step can be challenging for archaeological proteins, when they are heavily contaminated or decayed. The remains of animal fur/leather objects from an early medieval burial in Trossingen (580 CE) from Southwest Germany were submitted to proteomics analysis for species identification. One leather sample (TS3) yielded enough proteins to be identified as cow using a urea-based extraction (method "U"), confirming the microscopic identification. But two other samples (TS1 and TS2), compacted in a greyish brittle matrix with embedded hair visible only under microscope, could not be characterized with that method. A series of tests was performed using reduction/alkylation with tris(2-carboxyethyl)phosphine/chloroacetamide at 95 °C directly on the matrix (method "95C"), with or without the use of paramagnetic beads as cleaning procedure (from the single-pot solid-phase-enhanced sample preparation or SP3). Hair keratins were best recovered in the fur samples when digestion was performed directly on the insoluble fraction after reduction/alkylation. For both samples TS1 and TS2, an ovicaprine species was identified, with TS1 firmly identified as sheep due to the exceptional preservation of keratins and keratin-associated proteins. The simplified protocol also showed improvements on the identification of collagen in the leather sample TS3. SIGNIFICANCE: North European burials had a strong tradition of bodies wrapped or covered in animal skins; textiles, furs, items of leather and other organic materials were essential parts of grave furnishings (as part of the deceased's clothing as well as grave goods) but are mostly only preserved as residues, uncharacterized layers or stains. Even well preserved finds like the waterlogged organic remains from Trossingen show strong limitations for visual identification. Because the traditional protocol was unable to extract proteins efficiently from the soil matrix in which the samples were embedded, a new method was devised that enabled the determination of the sampled fur remains as sheep and the leather fragments as cow leather. Analyses showed that the key step for accessing the proteins in the soiled archaeological samples was heating for 10 min at 95 °C with a solution of tris(2-carboxyethyl)phosphine/chloroacetamide (TCEP/CAA). The protocol proposed in this study offers to work on minute samples (1 mg of sample or less) and overcame the challenge of separating the proteins from their archaeological matrix. It offers interesting perspectives for archaeological sites or objects where clothing are suspected but hardly detectable, such as burial sites.

Mass spectral analysis of acetylated peptides: Implications in proteomics

Sequence determination of peptides using mass spectrometry plays a crucial role in the bottom-up approaches for the identification of proteins. It is crucially important to minimise false detection and validate sequence of the peptides in order to correctly identify a protein. Chemical modification of peptides followed by mass spectrometry is an option for improving the spectral quality. In silico-derived tryptic peptides with different N-terminal amino acids were designed from human proteins and synthesized. The effect of acetylation on the fragmentation of peptides was studied. N-terminal acetylation of the tryptic peptides was shown to form b₁-ions, improve the abundance and occurrence of b-ions. In some cases, the intensity and occurrence of some y-ions also varied. Thus, it is demonstrated that acetylation plays an important role in improving the de novo sequencing efficiency of the peptides. The acetylation method was extended to tryptic peptides generated from the proteome of an Antarctic bacterium Pseudomonas syringae Lz4W using the proteomics work flow and mass spectra of the peptides were analysed. Comparison of the MS/MS spectra of the acetylated and unacetylated peptides revealed that acetylation helped in improving the spectral quality and validated the peptide sequences. Using this method, 673 proteins of the 1070 proteins identified were validated.

Characterization of acetylated histidine b1-ion structure: A competition between oxazolone and side chain imidazole moiety

The detection of post-translational modifications of proteins is an important comprehensive research area. Over the years, proteomic studies involving protein acetylation have attracted a great deal of attention. In the present study, we have focussed on the acetylation of histidine and the intrinsic stability of b₁-ion of oxazolone ring and/or with side chain imidazole bicyclic product. The formation of oxazolone structure may occur when an amino moiety undergoes acetylation reaction and when it is present in the vicinity of the side chain imidazole moiety. Tryptic peptides generated from the proteins of Acenitobacter radioresistens MMC5-containing N-terminal histidine were explored in a standard proteomic workflow. Formation of [Formula: see text] ion with an oxazolone ring in these peptides has been supported by a tandem mass spectrometric study of a synthetic peptide and density functional theory calculations. The results obtained from this study have implications in understanding the fragmentation of the peptides generated in the proteomic workflows.

A novel triplex isobaric termini labeling quantitative approach for simultaneously supplying three quantitative sources

Benefiting from high sensitivity and great ability to measure multiple samples simultaneously, isobaric tandem Mass spectrometry (MS2) quantification has been widely applied for protein biomarker screening. Here, a newly developed isobaric MS2 quantification method named triplex quantification by isobaric termini labeling (Triplex-QITL) was established. This method enables the accurate comparison of various fragment ions (reporter ions, amino acid fragments and N-/C-terminal fragments) based quantification to be operated in a single run. To our knowledge, this is the first time that this kind of comparison is achieved. In Triplex-QITL, proteins were first digested with Lys-C to produce peptides with lysine (K) at the C-termini, then dimethylation reagents and mTRAQ reagents were used to label the N-termini and C-termini of the peptides respectively. N- and C-terminal fragment ion pairs, reporter ions from mTRAQ (113,117,121) and a₁ ion pairs were simultaneously generated in MS2 spectra. In simple sample experiment, not much difference in using various fragment ions for quantification was observed. When analyzing SW480 cell lysate, comparing with a1 ions, about two times of reproducible quantification results were achieved by reporter ions and N- and C-terminal ions. Meanwhile the measured quantification results were much closer to the expected results even in large ratios (1:10:10) using N- and C-terminal ions. Finally, Triplex-QITL was successfully applied to profile metastatic differences of three hepatocellular carcinoma (HCC) cell lines. In all, Triplex-QITL shows a promising future in quantitative proteomics.

Integration of high accuracy N-terminus identification in peptide sequencing and comparative protein analysis via isothiocyanate-based isotope labeling reagent with ESI ion-trap TOF MS

A multifunctional isothiocyanate-based isotope labeling reagent, [d (0)]-/[d (6)]-4,6-dimethoxy pyrimidine-2-isothiocyanate (DMPITC), has been developed for accurate N-terminus identification in peptide sequencing and comparative protein analysis by ESI Ion-trap TOF mass spectrometry. In contrast with the conventional labeling reagent phenyl isothiocyanate (PITC), DMPITC showed more desirable properties such as rapid labeling, sensitivity enhancement, and facilitating peptide sequencing. More significantly, DMPITC-based labeling strategy possessed the capacity of higher reliable N-terminus identification owning to the high-yield b(1) ion combined with the isotope validation of 6 Da. Meanwhile, it also showed potential in differentiating isomeric residues of leucine and isoleucine at N-terminus on the basis of the relative abundance ratios between the fragment ions of their respective b(1) ions. The strategy not only allows accurate interpretation for peptide but also ensures rapid and sensitive comparative analysis for protein by direct MS analysis. Using trypsin-digested bovine serum albumin (BSA), both peptide N-terminus identification and quantitative analysis were accomplished with high accuracy, efficiency, and reproducibility. The application of DMPITC-based labeling strategy is expected to serve as a promising tool for proteome research.

Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W

Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.

Mapping N-terminus phosphorylation sites and quantitation by stable isotope dimethyl labeling

We have previously coupled stable isotope dimethyl labeling with IMAC enrichment for quantifying the extent of protein phosphorylation in vivo. The enhanced a(1) signal of dimethylated peptides served as a unique mass tag for unequivocal identification of the N-terminal amino acids. In this study, we demonstrate that the a(1) ion could further assist in mapping the precise phosphorylation site near the N-terminal region and allow the determination of the exact site and level of phosphorylation in one step by stable isotope dimethyl labeling. We show that the a(1) ion signal was suppressed for dimethylated peptides with a phosphorylation site at the N-terminus Ser/Thr residue (N-p*Ser/Thr) but was still enhanced for N-terminus Tyr residue (N-p*Tyr) or internal Ser/Thr residues (-p*Ser/Thr). Based on the dominant de-phosphorylated molecular ions and b-H(3)PO(4) ions for N-p*Ser/Thr, we propose that dimethyl labeling increases the basicity of the N-terminus and accelerates the de-phosphorylation for N-p*Ser/Thr precursors, which, however, suppresses the a(1) ion enhancement due to the resulting unsaturated covalent bond on C(alpha) of the N-terminus amino acid. Using this method, we excluded three Ser/Thr phosphorylation sites in A431 cells, two of which, however, were previously reported to be phosphorylation sites; we confirmed three known phosphorylation sites in A431 cells and quantified their ratios upon EGF treatment. Notably, we identified a novel phosphorylation site on Ser43 residue at N-terminus of the tryptic peptide derived from SVH protein in pregnant rat uteri. SVH protein has not been reported or implied with any phosphorylation event, and our data show that the Ser43 of SVH is an intrinsic phosphorylation site in pregnant rat uteri and that its phosphorylation level was slightly decreased upon c-AMP treatment.

Acetylating Tryptic Peptides Enhances b Ion Intensity in MALDI TOF/TOF: Implications in Peptide Sequencing and Identification of Proteins in an Antarctic Bacterium Pseudomonas Syringae

Several approaches have been described to identify proteins from MALDI MS/MS mass spectra. The sequence of tryptic peptides is determined by database searching or by de novo sequencing. Different algorithms are available to determine peptide sequence using mass spectra. False discovery of peptides is an associated problem with it. A combination of chemical modifications followed by mass spectral analysis helps in overcoming this problem. Acetylating the tryptic peptides of β-galactosidase in methanol is found to increase the b-ion signal intensity in MALDI TOF mass spectrometry. The method of acetylation is extended to the tryptic peptides of the proteins of an Antarctic bacterium Pseudomonas syringae, whose genome sequence is not known. These proteins are identified by searching the available database of the Pseudomonas spp at NCBI using the MS/MS spectra. The sequences of the peptides are validated using the CID mass spectra of the acetylated tryptic peptides.