Label-free quantitative proteomics of two Bifidobacterium longum strains.

Bifidobacteria are gram-positive anaerobes with a high Guanine/Cytosine genome content. Specific strains are used as probiotics because of their health benefits. Probiotics are live microorganisms with a positive influence on their host's health. They are used as nutritional supplements and their resistance to conditions of food manufacturing and of the gastro-intestinal tract is studied. We report on differential proteomics of two Bifidobacterium longum strains that differ in their heat shock resistance. This was achieved by a comparative qualitative survey of their proteomes and relative LC-MS/MS-based label-free protein quantification. Deploying a nano LC-ESI ion-trap mass spectrometer, 165 proteins expressed by the two probiotic strains were identified. Around 50% of these were common to both strains with the remaining half identified in either one of the strains. Using a label-free technology based on the 3D overlay of retention times, mass-over-charge ratios and ion intensities between LC-MS runs, we found quantitative differences in the relative abundance of 19 of the proteins common to both strains. The differentially expressed proteins were classified into categories involving glucose metabolism, protein synthesis and heat shock proteins. Six of these 19 proteins have been previously reported as being associated to heat stress response.

Combining protein identification and quantification: C-terminal isotope-coded tagging using sulfanilic acid.

Two methods of differential isotopic coding of carboxylic groups have been developed to date. The first approach uses d0- or d3-methanol to convert carboxyl groups into the corresponding methyl esters. The second relies on the incorporation of two 18O atoms into the C-terminal carboxylic group during tryptic digestion of proteins in H(2)18O. However, both methods have limitations such as chromatographic separation of 1H and 2H derivatives or overlap of isotopic distributions of light and heavy forms due to small mass shifts. Here we present a new tagging approach based on the specific incorporation of sulfanilic acid into carboxylic groups. The reagent was synthesized in a heavy form (13C phenyl ring), showing no chromatographic shift and an optimal isotopic separation with a 6 Da mass shift. Moreover, sulfanilic acid allows for simplified fragmentation in matrix-assisted laser desorption/ionization (MALDI) due the charge fixation of the sulfonate group at the C-terminus of the peptide. The derivatization is simple, specific and minimizes the number of sample treatment steps that can strongly alter the sample composition. The quantification is reproducible within an order of magnitude and can be analyzed either by electrospray ionization (ESI) or MALDI. Finally, the method is able to specifically identify the C-terminal peptide of a protein by using GluC as the proteolytic enzyme.

Differentially isotope-coded N-terminal protein sulphonation: combining protein identification and quantification.

Most proteomic labelling technologies intend to improve protein quantification and/or facilitate (de novo) peptide sequencing. We present here a novel stable-isotope labelling method to simultaneously identify and quantify protein components in complex mixtures by specifically derivatizing the N-terminus of proteins with 4-sulphophenyl isothiocyanate (SPITC). Our approach combines protein identification with quantification through differential isotope-coded labelling at the protein N-terminus prior to digestion. The isotope spacing of 6 Da (unlabelled vs. six-fold 13C-labelled tag) between derivatized peptide pairs enables the detection on different MS platforms (MALDI and ESI). Optimisation of the reaction conditions using SPITC was performed on three model proteins. Improved detection of the N-terminally derivatized peptide compared to the native analogue was observed in negative-ion MALDI-MS. Simpler fragmentation patterns compared to native peptides facilitated protein identification. The 13C-labelled SPITC resulted in convenient peptide pair spacing without isotopic overlap and hence facilitated relative quantification by MALDI-TOF/TOF and LC-ESI-MS/MS. The combination of facilitated identification and quantification achieved by differentially isotope-coded N-terminal protein tagging with light/heavy SPITC represents, to our knowledge, a new approach to quantitative proteomics.

Cystatin C as a potential cerebrospinal fluid marker for the diagnosis of Creutzfeldt-Jakob disease.

The definite diagnosis of Creutzfeldt-Jakob disease (CJD), the most common form of human prion diseases, relies upon neuropathological data usually obtained at autopsy. In living patients, the diagnosis, based on suggestive clinical features and EEG abnormalities, can be aided by the detection of altered levels of isoforms of the 14-3-3 protein in the cerebrospinal fluid (CSF). However, the validity of this test has been recently challenged and the search for other, more reliable biomarkers for CJD remains highly desirable. The present study describes the identification of a new potential surrogate marker in the CSF of CJD-affected patients. A preliminary study employing surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF) technology highlighted a protein at 13.4 kDa in a small group (n = 8) of CJD-affected patients. Further analysis aimed at identifying this protein using cationic exchange chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed it to be cystatin C. Additional immunoblot assays confirmed that the level of cystatin C was significantly increased (p

Production of the antiviral proteins 2'5'oligoadenylate synthetase, PKR and Mx in interstitial cells and spermatogonia.

We report an in vitro analysis of the spatial pattern of production of three antiviral proteins (2'5'oligoadenylate synthetase, 2'5'AS; double-stranded RNA-activated protein kinase, PKR; and Mx protein, Mx) in the rat testis, in basal conditions and following stimulation with interferon (IFN) or Sendai virus. The two major constituents of interstitial tissue--Leydig cells and macrophages--constitutively produce 2'5' oligoadenylate synthetase (2'5'AS), PKR and Mx. Production of an isoform of 2'5'AS was induced following Leydig cells stimulation by the Sendai virus. The most immature germ cells, spermatogonia, were devoid of 2'5'AS whatever the type of stimulation, whereas IFN treatment induced Mx production and increased PKR production in this cell type. IFN stimulation strongly increased PKR production in all three cell types. This new set of data extends our previous investigations and demonstrates that the testis possesses an anti-viral defense system involving IFNs and IFN-induced anti-viral proteins.

A potential cerebrospinal fluid and plasmatic marker for the diagnosis of Creutzfeldt-Jakob disease.

The recent occurrence of the new variant of Creutzfeldt-Jakob disease (CJD), probably transmitted to humans by cattle affected by the bovine form of spongiform encephalopathy, has generated renewed interest in the clinical issues related to human spongiform encephalopathies. Using the current set of diagnostic tools, these rare but devastating conditions may be difficult to diagnose with accuracy before death. The objective of the present communication is to describe the discovery of a potential cerebrospinal fluid (CSF) and plasmatic marker of human transmissible spongiform encephalopathies. A preliminary two-dimensional electrophoresis approach highlighted a potential neurodegenerative disorder marker called the fatty acid binding protein, FABP. Its heart form, H-FABP, was investigated in a small group of CJD affected patients (n = 8 ) by an immunoassay approach. The amount of FABP appeared to be significantly (p< or = 0.05) increased in all tested samples. H-FABP detection could therefore be helpful as a blood screening test for a pre-mortem diagnosis of the disease and also to prevent the risk of iatrogenic transmission of CJD through blood transfusion.

Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session.

After the success of the mass spectrometry (MS) round table that was held at the first Swiss Proteomics Society congress (SPS'01) in Geneva, the SPS has organized a proteomics application exercise and allocated a full session at the SPS'02 congress. The main objective was to encourage the exchange of expertise in protein identification, with a focus on the use of mass spectrometry, and to create a bridge between the users' questions and the instrument providers' solutions. Two samples were sent to fifteen interested labs, including academic groups and MS hardware providers. Participants were asked to identify and partially characterize the samples. They consisted of a complex mixture of peptide/proteins (sample A) and an almost pure recombinant peptide carrying post-translational modifications (sample B). Sample A was an extract of snake venom from the species Bothrops jararaca. Sample B was a recombinant and modified peptide derived from the shrimp Penaeus vannamei penaeidin 3a. The eight labs that returned results reported the use of a wide range of MS instrumentation and techniques. They mentioned a variety of time and manpower allocations. The origin of sample A was generally identified together with a number of database protein entries. The difficulty of the sample identification lay in the incomplete knowledge of the Bothrops species genome sequence and is discussed. Sample B was generally and correctly identified as penaeidin. However, only one group reported the full primary structure. Interestingly, the approaches were again varied and are discussed in the text.