Computational prediction of proteotypic peptides

Evaluation of: Mallick P, Schirle M, Chen SS et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25(1), 125–131 (2007).

Mass spectrometry, the driving analytical force behind proteomics, is primarily used to identify and quantify as many proteins in a complex biological mixture as possible. While there are many ways to prepare samples, one aspect that is common to a vast majority of bottom-up proteomic studies is the digestion of proteins into tryptic peptides prior to their analysis by mass spectrometry. As correctly highlighted by Mallick and colleagues, only a few peptides are repeatedly and consistently identified for any given protein within a complex mixture. While the existence of these proteotypic peptides (to borrow the authors’ terminology) is well known in the proteomics community, there has never been an empirical method to recognize which peptides may be proteotypic for a given protein. In this study, the investigators discovered over 16,000 proteotypic peptides from a collection of over 600,000 peptide identifications obtained from four different analytical platforms. The study examined a number of physicochemical parameters of these peptides to determine which properties were most relevant in defining a proteotypic peptide. These characteristic properties were then used to develop computational tools to predict proteotypic peptides for any given protein within an organism.     

Computational prediction of proteotypic peptides for quantitative proteomics

Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using >600,000 peptide identifications generated by four proteomic platforms, we empirically identified >16,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with >85% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).     

Assigning statistical significance to proteotypic peptides via database searches

Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the underlying peptide is not present, due to single amino acid polymorphisms (SAPs) or post-translational modifications (PTMs), in the proteotypic peptide libraries searched. To address both issues simultaneously, we have extended RAId's knowledge database to include proteotypic information, utilized RAId's statistical strategy to assign statistical significance to proteotypic peptides, and modified RAId's programs to allow for consideration of proteotypic information during database searches. The extended database alleviates the coverage problem since all annotated modifications, even those that occurred within proteotypic peptides, may be considered. Taking into account the likelihoods of observation, the statistical strategy of RAId provides accurate E-value assignments regardless whether a candidate peptide is proteotypic or not. The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches.     

Thiol peptides from the aspartate transaminase of chicken heart cytosol

Aspartate transaminase from chicken heart cytosol was immobilized covalently on activated thiol-Sepharose and digested with trypsin. After washing, the thiol-containing peptides were eluted with 2-mercaptoethanol and further purified by gel-filtration and paper chromatography. Three pure cysteinyl peptides were isolated. One of them may be represented as Ile-(Asp, Met, Cys, Gly, Leu, Thr2)-Lys; this peptide is identical to the fragment comprizing residues 387--395 in the peptide chain of aspartate transaminase from pig heart cytosol. It thus contains a cysteine residue homologous to Cys-390 of the pig heart enzyme. The second cysteinyl peptide had the following composition and partial sequence: Tyr-Phe-Val-Ser-Glu-Gly-Phe-Glu-Leu-Phe (Cys, Ala, Glu, Ser2, Phe)Lys, which corresponds to the sequence 242--258 of the pig enzyme and thus contains a cysteine residue homologous to Cys-252. The third cysteinyl peptide was similar to the tryptic peptide of the pig enzyme containing Cys-191.     

Isolation of inhibin like peptides from human placenta

Two moieties of inhibin could be obtained by chromatography of partially purified preparations of inhibin from human placenta on Sephadex G-100, G-25 and ion exchange chromatography on diethylaminoethyl Sephadex A-50. The higher molecular weight moiety (14,000) designated as HPI-H appears to be similar to inhibin from human seminal plasma. While the lower molecular weight moiety (1500) designated as HPI-L appears to be similar to that of sheep testicular inhibin. The preparations from both human term placenta and human seminal plasma inhibited the binding of [¹²⁵I] human follicle stimulating hormone to rat testicular receptors. This effect of inhibins could be neutralized by antisera raised against corresponding polypeptide. Further these antibodies could neutralize endogenous inhibin resulting in 2 to 3 fold increase in serum follicle stimulating harmone levels, which could then be reversed by exogenous administration of the isolated inhibin preparations.     

Cardioinhibitory peptides from Limulus polyphemus: modulation of the neurogenic heart

Four neuropeptides have been isolated and sequenced from acetone extracts of brains of the horseshoe crab Limulus polyphemus. They belong to a newly discovered peptide family in invertebrates. A possible role of the four peptides from Limulus as cardioregulatory neurotransmitters has been tested on the isolated Limulus heart. Three of the peptides (DEGHKMLYFamide, GHSLLHFamide, and PDHHMMYFamide) produce dose-dependent decreases in both amplitude and rate of the heart contractions, whereas DHGNMLYFamide reduces only the amplitude of the heartbeat. All four peptides differ in threshold, potency and duration of their effects.Abbreviations DIC diisopropylcarbodiimide - DTT dithiotreitol - Fmoc 9-fluorenylmethyloxycarbonyl - GABA gamma amino butyric acid - HOBt N-hydroxybenzotriazole - HPLC high performance liquid chromatography - IBMX 3-isobutyl 1-methyl-xanthine - Lip-HP Limulus head peptide - LP Limulus peptide - TBTU 2-(1H-benzotriazole-1yl)-1,1,3,3,tetramethyluronium tetrafluoroborate - TFA trifluoroacetic acid - TLC thin-layer chromatography     

Novel lactoferrampin antimicrobial peptides derived from human lactoferrin

Human lactoferrampin is a novel antimicrobial peptide found in the cationic N-terminal lobe of the iron-binding human lactoferrin protein. The amino acid sequence that directly corresponds to the previously characterized bovine lactoferrin-derived lactoferrampin peptide is inactive on its own (WNLLRQAQEKFGKDKSP, residues 269-285). However, by increasing the net positive charge near the C-terminal end of human lactoferrampin, a significant increase in its antibacterial and Candidacidal activity was obtained. Conversely, the addition of an N-terminal helix cap (sequence DAI) did not have any appreciable effect on the antibacterial or antifungal activity of human lactoferrampin peptides, even though it markedly influenced that of bovine lactoferrampin. The solution structure of five human lactoferrampin variants was determined in SDS micelles and all of the structures display a well-defined amphipathic N-terminal helix and a flexible cationic C-terminus. Differential scanning calorimetry studies indicate that this peptide is capable of inserting into the hydrophobic core of a membrane, while fluorescence spectroscopy results suggest that a hydrophobic patch encompassing the single Trp and Phe residues as well as Leu, Ile and Ala side chains mediates the interaction between the peptide and the hydrophobic core of a phospholipid bilayer.     

Hormone-containing peptides from normal and goiter human thyroglobulins

A series of low iodine human thyroglobulin samples derived from colloid-rich goiter tissue was examined by HPLC mapping of tryptic digests and compared to normal human thyroglobulin. These samples ranged in iodine content from 2 to 8 gram-atoms of iodine (g.a. I) per mole and were not further iodinated in vitro. Peptides containing the principal hormonogenic sequence were detected using the long wavelength absorbance of the iodotyrosine derivatives at 325 nm. Two such peptides were isolated and sequenced. Their thyroxine content was confirmed by radioimmunoassay. The number of 325-nm-absorbing peaks was significantly lower in the normally iodinated human thyroglobulin than that observed the thyroglobulins of cattle and dog. This suggests a more restricted iodination in the human protein. Sodium dodecyl sulfate gel patterns of the reduced and alkylated proteins showed significant molecular size heterogeneity in all of the samples. Polypeptide fragments ranged in molecular size from approximately 330 to 45 kDa in the goiter derived material and from approximately 330 to 15 kDa in the normal human material. This difference between the proteins is consistent with earlier observations that peptides less than 45 kDa appear concomitantly with hormone formation. These data confirm that the human thyroglobulin molecule is capable of forming at least limited amounts of thyroid hormone at iodine levels as low as 4 g.a. I per mole. The hormone detected in this study was located at residue 5 near the amino terminus of the thyroglobulin molecule.     

Acid alpha-glucosidase from human heart

An alpha-glucosidase maximally active at acid pH has been purified from human heart some 2,600-fold and its properties compared to a purified alpha-glucosidase from human liver. Molecular weight was evaluated using three different analytical procedures. The effect of various cations was determined. Thermal lability was evaluated using three different substrates. Affinity and hydrolysis velocity constants for maltose, glycogen and 4-methylumbelliferyl-alpha-D-glucose were determined for both preparations at optimal hydrogen ion concentration. Inhibition studies were carried out using the disaccharide turanose. From this study, we conclude there are no significant differences in molecular weight or kinetic properties between the cardiac and hepatic alpha-glucosidase enzymes.     

Stepwise identification of potent antimicrobial peptides from human genome

The increasing incidence of hospital acquired infections caused by antibiotic resistant pathogens has led to an increase in morbidity and mortality, finding alternative antibiotics unaffected by resistance mechanisms is fundamentally important for treating this problem. Naturally occurring proteins usually carry short peptide fragments that exhibit noticeable biological activity against a wide variety of microorganisms such as bacteria, fungi and protozoa. Traditional discovery of such antimicrobially active fragments (i.e. antimicrobial peptides, AMPs) from protein repertoire is either random or led by chance. Here, we report the use of a rational protocol that combines in silico prediction and in vitro assay to identify potential AMPs with high activity and low toxicity from the entire human genome. In the procedure, a three-step inference strategy is first proposed to perform genome-wide analysis to infer AMPs in a high-throughput manner. By employing this strategy we are able to screen more than one million peptide candidates generated from various human proteins, from which we identify four highly promising samples, and subsequently their antibacterial activity on five strains as well as cytotoxicity on human myoblasts are tested experimentally. As a consequence, two high-activity, low-toxicity peptides are discovered, which could be used as the structural basis to further develop new antibiotics. In addition, from 1491 known AMPs we also derive a quantitative measure called antibacterial propensity index (API) for 20 naturally occurring amino acids, which shows a significant allometric correlation with the theoretical minimal inhibitory concentration of putative peptides against Gram-positive and Gram-negative bacteria. This study may provide a proof-of-concept paradigm for the genome-wide discovery of novel antimicrobial peptides by using a combination of in silico and in vitro analyses.     

Heparin binding peptides co-purify with glycosaminoglycans from human plasma

Glycosaminoglycans (GAGs) are complexed with plasma proteins and proteolysis of plasma reduced the protein-GAG ratio about 140-fold. After dialysis, analysis by gradient PAGE revealed heparinase-1-sensitive GAGs, thus suggesting that heparin could be among the plasma GAGs. However, after dialysis most of the plasma GAGs were still not 'free'. PAGE of peptides resistant to proteolysis showed high molecular weight bands on the two sides of the dialysis membrane despite the 3.5 kDa molecular weight cut-off. Progressive dilution of the sample allowed passage of peptides appearing as high molecular weight bands in the diffusate. We interpret this phenomenon as the presence of low molecular weight peptides that aggregate when concentrated. Peptides on both sides of the membranes bound heparin.     

Isolation and characterization of histamine-releasing peptides from human parotid saliva

Peptides responsible for releasing histamine were purified from human parotid saliva. The amino acid composition of the peptides showed a high proportion of histidine, lysine and arginine. Molecular weights of these peptides were between 3000 and 5000 as determined by SDS-acrylamide gel electrophoresis. These peptides induced histamine release from rat-isolated mast cells accompanied with degranulation in a dose-dependent manner over the concentration range 5-50 micrograms/ml.