Unmatched masses in peptide mass fingerprints caused by cross-contamination: an updated statistical result

Wearable sampling of proteins from human exhaled aerosols for nano-liquid chromatography-tandem mass spectrometry analysis: A pilot study

RATIONALE

Human exhaled breath usually contains unique proteins that may provide clues to characterize individual physiological activities and many diseases. However, the concentration of exhaled proteins in exhaled breath is extremely low and usually does not reach the detection limits of all online breath mass spectrometry instruments. Therefore, developing a new breath sampler for collecting and characterizing exhaled proteins is important.

METHODS

In this study, a new mask-based wearable sampler was developed by fixing metal materials into the inner surface of the KN95 mask. Human exhaled proteins could be directly adsorbed onto the metal material while wearing the mask. After sampling, the collected proteins were eluted, digested, and identified using nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS).

RESULTS

The adsorption of exhaled proteins was evaluated, showing that modified gold foil is an effective material for collecting exhaled proteins. Various endogenous proteins were successfully identified from exhaled breath, many of which can be potential biomarkers for disease diagnosis.

CONCLUSIONS

By coupling the newly developed mask sampler with nano-LC-MS/MS, human exhaled proteins were successfully collected and identified. Our results show that the mask sampler is wearable, simple, and convenient, and the method is noninvasive for investigating disease diagnosis and human health.

Exhaled breath condensate for lung cancer protein analysis: a review of methods and biomarkers

Lung cancer is a leading cause of cancer-related deaths worldwide, and is considered one of the most aggressive human cancers, with a 5 year overall survival of 10-15%. Early diagnosis of lung cancer is ideal; however, it is still uncertain as to what technique will prove successful in the systematic screening of high-risk populations, with the strongest evidence currently supporting low dose computed tomography (LDCT). Analysis of exhaled breath condensate (EBC) has recently been proposed as an alternative low risk and non-invasive screening method to investigate early-stage neoplastic processes in the airways. However, there still remains a relative paucity of lung cancer research involving EBC, particularly in the measurement of lung proteins that are centrally linked to pathogenesis. Considering the ease and safety associated with EBC collection, and advances in the area of mass spectrometry based profiling, this technology has potential for use in screening for the early diagnosis of lung cancer. This review will examine proteomics as a method of detecting markers of neoplasia in patient EBC with a particular emphasis on LC, as well as discussing methodological challenges involving in proteomic analysis of EBC specimens.

Protein expression of sensory and motor nerves: Two-dimensional gel electrophoresis and mass spectrometry

The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product (gi|55628), glyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylglutathione lyase, adenylate kinase isozyme 1, two unnamed proteins products (gi|55628 and gi|1334163), and poly(rC)-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

[The study of protease primary specificity by statistical analysis of MALDI mass-spectra of proteolysis products]

Experimental verification for studying of proteolytic enzymes' primary specificity by statistical analysis of MALDI (matrix-assisted laser desorption/ionization) mass spectra of products obtained by protein substrates proteolysis was done by the use of proteinases with known substrate specificity (trypsin and glutamylendopeptidase). Proposed technique not requires direct determination of proteolysis products amino acid sequences, reliably establishes proteinases with anarrow substrate specificity and shows a relative tolerance for the presence in MALDI mass-spectra peaks of contaminants. It was shown that the pseudo-positive results exception requires the use of protein substrates series with the following averaging received statistical data.

Protein profile of exhaled breath condensate determined by high resolution mass spectrometry

A method based on liquid chromatography/high resolution tandem mass spectrometry coupled with electrophoretic separation, for determination and relative quantification of the protein composition of exhaled breath condensate (EBC), was developed. Application of the procedure to a sample of EBC, pooled from nine healthy subjects, resulted in the identification of 167 unique gene products, 113 of which not previously reported in EBC samples. The abundance of the protein identified was estimated by means of the exponentially modified protein abundance index protocol (emPAI). Cytokeratins were by far the most abundant proteins in EBC samples. Many of the identified proteins were associated with multiple cellular location with cytoplasm constituting the largest group. Cytosol, nucleus, membrane, cytoskeleton and extracellular were other abundantly represented locations. No amylase was detected, suggesting the absence of saliva protein contamination. The profile obtained represents the most comprehensive protein characterization of EBC so far reported and demonstrates that this approach provides a powerful tool for investigating the protein profile of EBC samples. Compared with analogous investigations, this study also shows that the protein profile of EBC is strongly affected by the sampling method adopted.

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques

BACKGROUND

Mass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant proportion of the peaks in a spectrum remain unexplained. In this paper we explore how a specific class of data mining techniques termed "frequent itemset mining" can be employed to discover patterns in the unassigned data, and how such patterns can help us interpret the origin of the unexpected/unexplained peaks.

RESULTS

First a model is proposed that describes the origin of the observed peaks in a mass spectrum. For this purpose we use the classical correlative database search algorithm. Peaks that support a positive identification of the spectrum are termed explained peaks. Next, frequent itemset mining techniques are introduced to infer which unexplained peaks are associated in a spectrum. The method is validated on two types of experimental proteomic data. First, peptide mass fingerprint data is analyzed to explain the unassigned peaks in a full scan mass spectrum. Interestingly, a large numbers of experimental spectra reveals several highly frequent unexplained masses, and pattern mining on these frequent masses demonstrates that subsets of these peaks frequently co-occur. Further evaluation shows that several of these co-occurring peaks indeed have a known common origin, and other patterns are promising hypothesis generators for further analysis. Second, the proposed methodology is validated on tandem mass spectrometral data using a public spectral library, where associations within the mass differences of unassigned peaks and peptide modifications are explored. The investigation of the found patterns illustrates that meaningful patterns can be discovered that can be explained by features of the employed technology and found modifications.

CONCLUSIONS

This simple approach offers opportunities to monitor accumulating unexplained mass spectrometry data for emerging new patterns, with possible applications for the development of mass exclusion lists, for the refinement of quality control strategies and for a further interpretation of unexplained spectral peaks in mass spectrometry and tandem mass spectrometry.

Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum

The black Périgord truffle (Tuber melanosporum Vittad.) is a highly prized food today, with its unique scent (i.e., perfume) and texture. Despite these attributes, it remains relatively poorly studied, lacking "omics" information to characterize its biology and biochemistry, especially changes associated with freshness and the proteins/metabolites responsible for its organoleptic properties. In this study, we have functionally annotated the truffle proteome from the 2010 T. melanosporum genome comprising 12,771 putative nonredundant proteins. Using sequential BLAST search strategies, we identified homologues for 2587 proteins with 2486 (96.0%) fungal homologues (available from http://biolinfo.org/protannotator/blacktruffle.php). A combined 1D PAGE and high-accuracy LC-MS/MS proteomic study was employed to validate the results of the functional annotation and identified 836 (6.5%) proteins, of which 47.5% (i.e., 397) were present in our bioinformatics studies. Our study, functionally annotating 6487 black Périgord truffle proteins and confirming 836 by proteomic experiments, is by far the most comprehensive study to date contributing significantly to the scientific community. This study has resulted in the functional characterization of novel proteins to increase our biological understanding of this organism and to uncover potential biomarkers of authenticity, freshness, and perfume maturation.

Collagen-cellulose composite thin films that mimic soft-tissue and allow stem-cell orientation

Mechanical properties of collagen films are less than ideal for biomaterial development towards musculoskeletal repair or cardiovascular applications. Herein, we present a collagen-cellulose composite film (CCCF) compared against swine small intestine submucosa in regards to mechanical properties, cell growth, and histological analysis. CCCF was additionally characterized by FE-SEM, NMR, mass spectrometry, and Raman Microscopy to elucidate its physical structure, collagen-cellulose composition, and structure activity relationships. Mechanical properties of the CCCF were tested in both wet and dry environments, with anisotropic stress-strain curves that mimicked soft-tissue. Mesenchymal stem cells, human umbilical vein endothelial cells, and human coronary artery smooth muscle cells were able to proliferate on the collagen films with specific cell orientation. Mesenchymal stem cells had a higher proliferation index and were able to infiltrate CCCF to a higher degree than small intestine submucosa. With the underlying biological properties, we present a collagen-cellulose composite film towards forthcoming biomaterial-related applications.

Attempting to distinguish between endogenous and contaminating cytokeratins in a corneal proteomic study

BACKGROUND

The observation of cytokeratins (CK's) in mass spectrometry based studies raises the question of whether the identified CK is a true endogenous protein from the sample or simply represents a contaminant. This issue is especially important in proteomic studies of the corneal epithelium where several CK's have previously been reported to mark the stages of differentiation from corneal epithelial stem cell to the differentiated cell.

METHODS

Here we describe a method to distinguish very likely endogenous from uncertain endogenous CK's in a mass spectrometry based proteomic study. In this study the CK identifications from 102 human corneal samples were compared with the number of human CK identifications found in 102 murine thymic lymphoma samples.

RESULTS

It was anticipated that the CK's that were identified with a frequency of <5%, i.e. in less than one spot for every 20 spots analysed, are very likely to be endogenous and thereby represent a 'biologically significant' identification. CK's observed with a frequency >5% are uncertain endogenous since they may represent true endogenous CK's but the probability of contamination is high and therefore needs careful consideration. This was confirmed by comparison with a study of mouse samples where all identified human CK's are contaminants.

CONCLUSIONS

CK's 3, 4, 7, 8, 11, 12, 13, 15, 17, 18, 19, 20 and 23 are very likely to be endogenous proteins if identified in a corneal study, whilst CK's 1, 2e, 5, 6A, 9, 10, 14 and 16 may be endogenous although some are likely to be contaminants in a proteomic study. Further immunohistochemical analysis and a search of the current literature largely supported the distinction.

Proteomic profile of primary isolated rat mesangial cells in high-glucose culture condition and decreased expression of PSMA6 in renal cortex of diabetic rats

Diabetic nephropathy (DN) is one of the most important complications of diabetic patients and is characterized histologically by an accumulation of extracellular matrix (ECM) protein in the glomerular mesangium. Therefore, mesangial cells likely play an important role in the development of diabetic nephropathy. Here, we employed proteomic techniques to investigate the protein profile of rat mesangial cells under high-glucose culture conditions. Primary isolated rat glomerular mesangial cells were cultured under different concentrations of glucose (5.4 mmol.L-1 for normal control and 30 mmol.L-1 for high glucose) for 0, 8, 16, and 72 h, as well as for 25 days. Cellular total proteins were isolated from these cells and employed for two-dimensional gel electrophoresis (2-DE). Differentially expressed proteins were identified by matrix-assisted laser desorption - ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and some of these proteins were documented in rat models of diabetes by Western blot. Rat mesangial cells were successfully isolated in the laboratory and their proliferation rates were significantly inhibited by high glucose. Two-dimensional gel electrophoresis analyses revealed 28 differentially expressed protein spots between the normal and high-glucose groups. After MALDI-TOF-MS analysis, all 28 protein spots were successfully identified with the peptide mass fingerprint (PMF) method. Representatively, SOD1, PCBP1 and PSMA6 were validated by Western blot analysis following protein extractions from the normal and high-glucose groups. Abundance of these proteins was consistent with that found in 2-DE. Moreover, expression of SOD1, PCBP1, and PSMA6 in renal cortex was further examined in two rat models of diabetes (streptozotocin-induced and spontaneous OLETF diabetic models). Abundance of SOD1 and PCBP1 proteins did not show any significant difference between normal control and diabetic rats. However, abundance of the PSMA6 protein was significantly reduced in the renal cortex of both STZ-induced and spontaneous OLETF diabetic rats. Proteomic analysis identified 28 differentially expressed proteins in primary isolated rat mesangial cells between normal and high glucose treatments. Expression of one identified protein was found to be consistent with expression in the renal cortex of two rat diabetic models. Therefore, identification of protein expression patterns in mesangial cells can be employed to develop a therapeutic target for treatment of diabetic nephropathy.

Proteomic analysis of proteins selectively associated with hydroxyapatite, brushite, and uric acid crystals precipitated from human urine

The aim of this study was to compare the intracrystalline protein profiles of hydroxyapatite (HA), brushite (BR), and uric acid (UA) crystals precipitated from the same urine samples. HA, BR, and UA crystals were precipitated on two different occasions from the same pooled healthy urine. Crystals were washed to remove surface-bound proteins, and their composition was confirmed using Fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FESEM) coupled with energy dispersive X-ray analysis (EDAX). SDS-PAGE was used for visual comparison of the protein content of the demineralised crystal extracts, which were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). HA comprised nanosized particles interspersed with organic material, which was absent from the BR and UA crystals. The number and type of individual proteins differed between the 3 minerals: 45 proteins were detected in the HA crystal extracts and 77 in the BR crystals, including a number of keratins, which were regarded as methodological contaminants. After excluding the keratins, 21 proteins were common to both HA and BR crystals. Seven nonkeratin proteins were identified in the UA extracts. Several proteins consistently detected in the HA and BR crystal extracts have been previously implicated in kidney stone disease, including osteopontin, prothrombin, protein S100A9 (calgranulin B), inter-α-inhibitor, α1-microglobulin bikunin (AMBP), heparan sulfate proteoglycan, and Tamm-Horsfall glycoprotein, all of which are strong calcium binders. We concluded that the association of proteins with HA, BR, and UA crystals formed in healthy urine is selective and that only a few of the numerous proteins present in healthy urine are likely to play any significant role in preventing stone pathogenesis.

Improving mass defect filters for human proteins

The mass defect of a substance can be used in mass spectral analysis to identify peaks as likely belonging to a compound class, such as peptides, if the mass defect is within the known range for that compound class. For peptides, a range of possible mass defects was calculated previously, using a set of theoretical peptides, where all possible amino acid combinations were considered (Mann , M. Abstract from the 43(rd) Annual Conference on Mass Spectrometry and Allied Topics; Conference Proceedings , 1995). We compare that range of theoretical peptide mass defects to new values obtained from in silico tryptic digests of proteins that are abundant in human serum and human seminal fluid. The range of mass defect values encompassing 95% of peptides for the human protein data sets was found to be up to 50% smaller than the previously reported mass defect range for the theoretical peptides. The smaller range established for human tryptic peptides can be used to improve peptide mass defect filters by excluding more species that are not likely to be peptides, thus improving filter selectivity for peptides during proteomic data analysis.

The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure

The 5'-end of the flavivirus genome harbors a methylated (m7)GpppA(2'OMe) cap structure, which is generated by the virus-encoded RNA triphosphatase, RNA (guanine-N7) methyltransferase, nucleoside 2'-O-methyltransferase, and RNA guanylyltransferase. The presence of the flavivirus guanylyltransferase activity in NS5 has been suggested by several groups but has not been empirically proven. Here we provide evidence that the N-terminus of the flavivirus NS5 protein is a true RNA guanylyltransferase. We demonstrate that GTP can be used as a substrate by the enzyme to form a covalent GMP-enzyme intermediate via a phosphoamide bond. Mutational studies also confirm the importance of a specific lysine residue in the GTP binding site for the enzymatic activity. We show that the GMP moiety can be transferred to the diphosphate end of an RNA transcript harboring an adenosine as the initiating residue. We also demonstrate that the flavivirus RNA triphosphatase (NS3 protein) stimulates the RNA guanylyltransferase activity of the NS5 protein. Finally, we show that both enzymes are sufficient and necessary to catalyze the de novo formation of a methylated RNA cap structure in vitro using a triphosphorylated RNA transcript. Our study provides biochemical evidence that flaviviruses encode a complete RNA capping machinery.

A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues

A comparative study of proteome and transcriptome changes during Medicago truncatula (cultivar Jemalong) seed development has been carried out. Transcript and protein profiles were parallel across the time course for 50% of the comparisons made, but divergent patterns were also observed, indicative of post-transcriptional events. These data, combined with the analysis of transcript and protein distribution in the isolated seed coat, endosperm, and embryo, demonstrated the major contribution made to the embryo by the surrounding tissues. First, a remarkable compartmentalization of enzymes involved in methionine biosynthesis between the seed tissues was revealed that may regulate the availability of sulfur-containing amino acids for embryo protein synthesis during seed filling. This intertissue compartmentalization, which was also apparent for enzymes of sulfur assimilation, is relevant to strategies for modifying the nutritional value of legume seeds. Second, decreasing levels during seed filling of seed coat and endosperm metabolic enzymes, including essential steps in Met metabolism, are indicative of a metabolic shift from a highly active to a quiescent state as the embryo assimilates nutrients. Third, a concomitant persistence of several proteases in seed coat and endosperm highlighted the importance of proteolysis in these tissues as a supplementary source of amino acids for protein synthesis in the embryo. Finally, the data revealed the sites of expression within the seed of a large number of transporters implied in nutrient import and intraseed translocations. Several of these, including a sulfate transporter, were preferentially expressed in seeds compared with other plant organs. These findings provide new directions for genetic improvement of grain legumes.

Exercise affects energy metabolism and neural plasticity-related proteins in the hippocampus as revealed by proteomic analysis

Studies were conducted to evaluate the effect of a brief voluntary exercise period on the expression pattern and post-translational modification of multiple protein classes in the rat hippocampus using proteomics. An analysis of 80 protein spots of relative high abundance on two-dimensional gels revealed that approximately 90% of the proteins identified were associated with energy metabolism and synaptic plasticity. Exercise up-regulated proteins involved in four aspects of energy metabolism, i.e. glycolysis, ATP synthesis, ATP transduction and glutamate turnover. Specifically, we found increases in fructose-bisphosphate aldolase C, phosphoglycerate kinase 1, mitochondrial ATP synthase, ubiquitous mitochondrial creatine kinase and glutamate dehydrogenase 1. Exercise also up-regulated specific synaptic-plasticity-related proteins, the cytoskeletal protein alpha-internexin and molecular chaperones (chaperonin-containing TCP-1, neuronal protein 22, heat shock 60-kDa protein 1 and heat shock protein 8). Western blot was used to confirm the direction and magnitude of change in ubiquitous mitochondrial creatine kinase, an enzyme essential for transducing mitochondrial-derived ATP to sites of high-energy demand such as the synapse. Protein phosphorylation visualized by Pro-Q Diamond fluorescent staining showed that neurofilament light polypeptide, glial fibrillary acidic protein, heat shock protein 8 and transcriptional activator protein pur-alpha were more intensely phosphorylated with exercise as compared with sedentary control levels. Our results, together with the fact that most of the proteins that we found to be up-regulated have been implicated in cognitive function, support a mechanism by which exercise uses processes of energy metabolism and synaptic plasticity to promote brain health.

Mass Spectrometric Analysis of Glycine Receptor-associated Gephyrin Splice Variants

Gephyrin is an ubiquitously expressed protein that, in the nervous system, is essential for synaptic anchoring of glycine receptors (GlyRs) and major GABAA receptor subtypes. The binding of gephyrin to the GlyR depends on an amphipathic motif within the large intracellular loop of the GlyRbeta subunit. The mouse gephyrin gene consists of 30 exons. Ten of these exons, encoding cassettes of 5-40 amino acids, are subject to alternative splicing (C1-C7, C4'-C6'). Since one of the cassettes, C5', has recently been reported to exclude GlyRs from GABAergic synapses, we investigated which cassettes are found in gephyrin associated with the GlyR. Gephyrin variants were purified from rat spinal cord, brain, and liver by binding to the glutathione S-transferase-tagged GlyRbeta loop or copurified with native GlyR from spinal cord by affinity chromatography and analyzed by mass spectrometry. In addition to C2 and C6', already known to be prominent, C4 was found to be abundant in gephyrin from all tissues examined. The nonneuronal cassette C3 was easily detected in liver but not in GlyR-associated gephyrin from spinal cord. C5 was present in brain and spinal cord polypeptides, whereas C5' was coisolated mainly from liver. Notably C5'-containing gephyrin bound to the GlyRbeta loop, inconsistent with its proposed selectivity for GABAA receptors. Our data show that GlyR-associated gephyrin, lacking C3, but enriched in C4 without C5, differs from other neuronal and nonneuronal gephyrin isoforms.

The tegument surface membranes of the human blood parasite Schistosoma mansoni: a proteomic analysis after differential extraction

The blood fluke Schistosoma mansoni can live for years in the hepatic portal system of its human host and so must possess very effective mechanisms of immune evasion. The key to understanding how these operate lies in defining the molecular organisation of the exposed parasite surface. The adult worm is covered by a syncytial tegument, bounded externally by a plasma membrane and overlain by a laminate secretion, the membranocalyx. In order to determine the protein composition of this surface, the membranes were detached using a freeze/thaw technique and enriched by sucrose density gradient centrifugation. The resulting preparation was sequentially extracted with three reagents of increasing solubilising power. The extracts were separated by 2-DE and their protein constituents were identified by MS/MS, yielding predominantly cytosolic, cytoskeletal and membrane-associated proteins, respectively. After extraction, the final pellet containing membrane-spanning proteins was processed by liquid chromatographic techniques before MS. Transporters for sugars, amino acids, ions and other solutes were found together with membrane enzymes and proteins concerned with membrane structure. The proteins identified were categorised by their function and putative location on the basis of their homology with annotated proteins in other organisms.

Proteome analysis of up-regulated proteins in the rat spinal cord induced by transection injury

The inability of the CNS to regenerate in adult mammals propels us to reveal associated proteins involved in the injured CNS. In this paper, either thoracic laminectomy (as sham control) or thoracic spinal cord transection was performed on male adult rats. Five days after surgery, the whole spinal cord tissue was dissected and fractionated into water-soluble (dissolved in Tris buffer) and water-insoluble (dissolved in a solution containing chaotropes and surfactants) portions for 2-DE. Protein identification was performed by MS and further confirmed by Western blot. As a result, over 30 protein spots in the injured spinal cord were shown to be up-regulated no less than 1.5-fold. These identified proteins possibly play various roles during the injury and repair process and may be functionally categorized as several different groups, such as stress-responsive and metabolic changes, lipid and protein degeneration, neural survival and regeneration. In particular, over-expression of 11-zinc finger protein and glypican may be responsible for the inhibition of axonal growth and regeneration. Moreover, three unknown proteins with novel sequences were found to be up-regulated by spinal cord injury. Further characterization of these molecules may help us come closer to understanding the mechanisms that underlie the inability of the adult CNS to regenerate.

Identification of novel proteases and immunomodulators in the secretions of schistosome cercariae that facilitate host entry

Schistosomiasis, caused by parasitic helminths, remains a serious human disease in the tropics. Cercariae of Schistosoma mansoni infect their hosts by direct skin penetration, aided by secretions from acetabular and head glands. Both proteolytic and immunomodulatory properties have been ascribed to the released material, but to date only five isoforms of elastase and one putative anti-inflammatory protein (Sm16) have been cloned. We analyzed secretions from mechanically transformed cercariae by two-dimensional electrophoresis. An average gel image was created and compared with a separation of soluble larval extract, revealing a less complex spot pattern in the secretions with 60% of the spots matched to the larval extract. Subsequent tandem mass spectrometric analysis identified 48 spots from the released material, representing approximately 80% of its normalized volume. Twenty-nine of these are likely to originate in the vesicles, and 18 are likely to originate in the cytosol of the glands (the latter class being present due to holocrine secretion); one is unknown. The vesicular proteins were significantly more enriched than the cytosolic proteins in the released material when compared with the larval extract. A novel metalloproteinase (termed SmPepM8) was the second most abundant constituent after three isoforms of cercarial elastase. In addition, a dipeptidyl peptidase IV (SmDPP IV) was discovered but in much smaller quantity. A new serine protease inhibitor (SmSerp_c) was also prominent. Along with Sm16, four potential immunomodulators were identified, three with similarity to venom allergens (SmSCP_a, _b, and _c) and one with homology to the potassium channel blockers in scorpion venom (SmKK7). Interrogation of the expressed sequence tag database found transcripts encoding the majority of vesicular proteins present solely in the intramolluscan stages of the life cycle. Distinct patterns of radiolabel incorporation suggested three separate origins for the vesicular proteins. All the novel constituents merit investigation as vaccine candidates, and the potential immunomodulators merit investigation as therapeutic agents.

An agent-based system to discover protein–protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints

Proteins "work together" by actually binding to form multicomponent complexes that carry out specific functions. Proteomic analyses based on the mass spectrum are now key methods to determine the components in protein complexes. The protein-protein interaction or functional association may be known to exist among the extracted protein spots while analyzing the proteins on the 2D gel. In this study, we develop an agent-based system, namely AgentMultiProtIdent, which integrated two protein identification tools and a variety of databases storing relations among proteins and used to discover protein-protein interactions and protein functional associations, and identify protein complexes and proteins with multiple peptide mass fingerprints as input. The system takes Multiple Peptide Mass Fingerprints (PMFs) as a whole in the protein complex or protein identification. With the relations among proteins, it may greatly improve the accuracy of identification of protein complexes. Also, possible relationship of the multiple peptide mass fingerprints, such as ontology relation, can be discovered by our system, especially in the identification of protein complexes. The agent-based system is now available on the Web at http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/.

Analysis of human multidrug resistance protein 1 (ABCC1) by matrix-assisted laser desorption ionization/time of flight mass spectrometry: toward identification of leukotriene C4 binding sites

Multidrug resistance in tumor cells may be caused by reduced drug accumulation resulting from expression of one or more proteins belonging to the ATP-binding cassette (ABC) transporter superfamily. In addition to their drug efflux properties, certain ABC proteins such as multidrug resistance protein 1 (MRP1) (ABCC1) mediate the ATP-dependent transport of a broad array of organic anions. The intrinsically photoreactive glutathione-conjugated cysteinyl leukotriene C4 (LTC4) is a high-affinity physiological substrate of MRP1 and is widely regarded as a model compound for evaluating the substrate binding and transport properties of wild-type and mutant forms of the transporter. In the present study, we have optimized high-level expression of recombinant human MRP1 in Pichia pastoris and developed a two-step purification scheme that results in purification of the transporter to >90% homogeneity. Peptide mapping by matrix-assisted laser desorption ionization/time of flight mass spectrometry of the peptides generated by in-gel protease digestions of purified underglycosylated MRP1 identified 96.7% of the MRP1 sequence with >98% coverage of its 17 transmembrane helices. Subsequent comparisons with mass spectra of MRP1 photolabeled with LTC4 identified six candidate LTC4-modified peptide fragments that are consistent with the conclusion that the intracellular juxtamembrane positions of transmembrane helices 6, 7, 10, 17, and a COOH-proximal portion of the cytoplasmic loop that links the first and second membrane spanning domains are part of the LTC4 binding site of the transporter. Our studies confirm the usefulness of mass spectrometry for analysis of mammalian polytopic membrane proteins and for identification of substrate binding sites of human MRP1.

MultiProtIdent: Identifying Proteins Using Database Search and Protein−Protein Interactions

Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.

Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis

Helicobacter pylori is a causative agent of severe diseases of the gastric tract ranging from chronic gastritis to gastric cancer. Cellular proteins of H. pylori were separated by high resolution two-dimensional gel electrophoresis. A dataset of 384 spots was automatically picked, digested, spotted, and analyzed by matrix-assisted laser desorption ionization mass spectrometry peptide mass fingerprint in triple replicates. This procedure resulted in 960 evaluable mass spectra. Using a new version of our data analysis software MS-Screener we improved identification and tested reliability of automatically generated data by comparing with manually produced data. Antigenic proteins from H. pylori are candidates for vaccines and diagnostic tests. Previous immunoproteomics studies of our group revealed antigen candidates, and 24 of them were now closely analyzed using the MS-Screener software. Only in three spots minor components were found that may have influenced their antigenicities. These findings affirm the value of immunoproteomics as a hypothesis-free approach. Additionally, the protein species distribution of the known antigen GroEL was investigated, dimers of the protein alkyl hydroperoxide reductase were found, and the fragmentation of gamma-glutamyltranspeptidase was demonstrated.