Enhanced Laser Desorption Ionization Time Research Articles

Epidemiological tools for effective surveillance of porcine cysticercosis in Africa

Porcine cysticercosis is widely distributed in developing countries. Many tools were developed for effective control of the tapeworm in endemic countries. Tongue examination, meat inspection and Ag-ELISA were widely used in epidemiological survey. Both tongue examination and meat inspection are highly specific but less sensitive. To improve performance of AgELISA, unambiguous test based on nanobodies was performed. Immunodiagnostic tests based on PCR, flows through assay (FTA), Surface Enhanced Laser Desorption–Ionization Time of Flight (SELDI-TOF) were also developed. Less data were reported using spatial statistical analysis hence multiples approaches were available for effective epidemiological survey of porcine cysticercosis.

Identification of diagnostic and prognostic biomarkers to improve the management of diabetes-related ulcers

IntroductionDiabetes-related ulcers are a common and severe complication of diabetes which is expected to increase in prevalence in line with projected global growth in rates of diabetes. Caring for these chronic wounds imposes a multi-billion dollar burden on the health care systems. These ulcers can prove lethal if untreated or not recognised and can lead to critical health complications. MethodsTo investigate underlying causes of wound chronicity, proteomic analyses of swab samples collected weekly from healing and non-healing diabetic foot ulcers was performed. Protein profiling was conducted based on Surface Enhanced Laser Desorption Ionisation Time of Flight (SELDI-TOF) mass spectrometry and statistical softwares were used to short list potential biomarkers. In addition, bottom-up proteomics was performed on healing and non-healing samples by SDS-PAGE and LC-MS/MS analysis using an AB SCIEX Triple TOF ® 5600 System. Trans-proteomic pipeline was used for data analyses and X! Tandem was used to search the database. Label-free quantitative proteomic analyses were performed using a computational tool called Abacus. Results(1) Statistical analyses of healing and non healing samples analysed on SELDI-TOF revealed 5 and 7 potential biomarkers (m/z) for samples with Texas score A1 and C1 respectively. (2) Bottom-up proteomics approach from both healing and non-healing samples identified 15 unique (healing) and 16 unique (non-healing) potential biomarkers. (3) Quantitative proteomic analyses resulted in 24 and 45 up-regulated healing candidates and 67 and 43 up-regulated nonhealing candidates for Texas score A1 and C1 wounds. (4) Relative quantification of 23 proteins related to oxidative stress has been identified through Abacus and 5/23 proteins have been validated using ELISA. ConclusionsWe are investigating these potential biomarkers using various biochemical, bioinformatics and statistical tools. A thorough investigation and study of the patterns may generate new protein candidates that can be used as potential prognostic and diagnostic biomarkers to improve the management of diabetic ulcers.

SELDI-TOF analysis of glioblastoma cyst fluid is an approach for assessing cellular protein expression

Objectives:In about 10% of glioblastoma patients, preoperative MRI discloses the presence of tumor cysts. Whereas the impact of cystic appearance on prognosis has been discussed extensively, only little is known about the tumor cyst fluid. In this study, we tested the feasibility of the surface enhanced laser desorption ionization time of flight (SELDI-TOF) technique to detect cyst fluid proteins.Methods:Cyst fluid was collected from 21 glioblastoma patients for SELDI-TOF analysis and compared to control cerebrospinal fluids from 15 patients with spinal stenosis. Resulting protein peaks with significant differences between groups were further described, using the molecular weight in an internet search of protein databases and publications. Two potential cyst fluid proteins, basigin and ferritin light chain, were selected for immunohistological detection in the histologic slides of the patients, metallothionein (MT) served as negative control.Results:As supposed from the results of the SELDI-TOF analysis, basigin and ferritin were detected immunohistochemically in the cyst wall, whereas MT was more equally distributed between the cyst wall and the surrounding tumor tissue. Median survival time of the patients was 20 months (range 2 to 102 months) and correlated with age, but not with expression of the three proteins.Discussion:The SELDI-TOF approach reveals a number of proteins, potentially present in glioblastoma cyst fluid. Identification of these proteins in tumor cells may help understand the pathogenetic pathways and the prognostic value of cystic changes.

Diagnosis model of idiopathic thrombocytopenic purpura based on platelet differential proteome

This study was purposed to establish a new quick and simple diagnostic method with high sensitivity and good specificity for idiopathic thrombocytopenic purpura (ITP) and to evaluate its significance. 240 platelet lysates (from patients with ITP, leukemia, MDS, and healthy adults, each of 60 cases) were randomly assigned to training set (120 cases) or validation set (120 cases), all of them were detected by surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS), in order to identify the differentially expressed protein, the diagnostic model was established by means of artificial neural network (ANN), and was validated by blind test with SPSS 17.0. The results showed that 5 marked proteins significantly differentially expressed (P < 0.01), m/z of highly expressed proteins were 2234.30, 3476.36, and 7526.29, m/z of low expressed proteins were 4990.02 and 5152.39, respectively. The sensitivity and specificity of diagnostic model were 80.6% and 77.3% respectively. The area under the ROC curve consisting of the output value of artificial neura1 network was 0.837. Efficacy of the model was validated by means of blinded test. It is concluded that the ANN model is useful for clinical diagnosis of ITP on the basis of platelet protein fingerprint spectrum.

Matrix Free Material Enhanced Laser Desorption Ionization Mass Spectrometric Analysis of Amino Acids in Althaea Officinalis, Matricaria Chamomilla, and Taraxacum Officinale

The standardization of natural product drugs needs reliable methods for the analysis of raw materials and final products. In this study, qualitative analysis of amino acids in herbal extracts was performed using mass spectrometric method, that is, matrix- free material enhanced laser desorption ionization time of flight mass spectrometry (mf-MELDI-MS). Samples employed in the study were standards and water extracts from Althaea officinalis, Taraxacum officinale, and Matricaria chamomilla. These analyses confirmed the presence of amino acids and clearly proved the adequate performance of mf-MELDI-MS for the qualitative analysis of complex mixtures, as targets do not need modification and analysis requires only a few minutes. Determination of amino acids in these plants were performed and reported for the first time using the modified silica gel (4,4′-azodianiline modified silica gel) and mf-MELDI-MS technique.

New analytical tools for quality control of natural products

Phytopharmacy with its huge variety and complexity of plants, extraction procedures and ingredients is a permanently demanding challenge for the analytical chemist. The separation of active components from natural products has become increasingly important and new advancements in chromatography allow exploring inaccessible areas of natural product isolation. There is a need for highly efficient techniques to handle the problems associated with sample preparation, separation and identification. Novel enrichment and purification methods based on modern SPE technologies are applied to reduce the complexity of plant materials while µ-HPLC is used for separation, preconcentration and fractionation. Recent research in the area of solid-phase extraction led to the development of novel stationary phases based on organic polymers and fullerene-silica for enrichment and purification of natural products. Considerable progress has been made in the development of stationary phases which can be tailored to a specific application allowing endless possibilities in terms of selectivity tuning. An analytical platform which allows to profile and characterize plant materials and their extractives by vibrational spectroscopy, infrared (IR) based imaging, CE-MS and matrix-free material enhanced laser desorption ionization time of flight mass spectrometry (mf-MELDI-TOF/MS) was established. Thereby, vibrational spectroscopy offers the advantages of fast, non-invasive and simultaneous determination of chemical and physical properties being suitable for high-throughput analytical quality control.

Disease Specific Biomarkers of Abdominal Aortic Aneurysms Detected by Surface Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry

IntroductionBiomarkers have the potential to improve the clinical management of patients with AAA. ReportA prospective, proteomics discovery study was undertaken to compare patients with AAA (n = 20) to matched screened controls (n = 19) for plasma protein expression. Surface-Enhanced-Laser-Desorption-Ionization Time of Flight Mass Spectrometry (SELDI ToF MS) coupled with Artificial Neural Networks (ANN) analysis identified six protein related diagnostic biomarker ions with a combined AUC of 0.89. DiscussionThis study discovered a signature plasma protein profile for patients with AAA and demonstrated that mass spectrometric based research for disease specific biomarker of AAA is feasible.

Effect of Turkish propolis extracts on proteome of prostate cancer cell line

BackgroundPropolis is a natural, resinous hive product that has several pharmacological activities. Its composition varies depending on the vegetation, climate, season and environmental conditions of the area from where it was collected. Surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF MS) is a proteomic approach which has been used in cancer proteomics studies. Prostate cancer is one of the most commonly diagnosed cancers in men. It has shown that nutritional supplements rich in polyphenolic compounds such as propolis play a significant role in prostate cancer chemoprevention. The aim of this study is to evaluate if protein expression profile in PC-3 prostate cancer cell lines could be differentiated when incubated with dimethyl sulfoxide and water extracts of Turkish propolis.ResultsThe antioxidant potentials of dimethyl sulfoxide and water extracts of propolis were found in correlation with the amount of total phenolic compounds of them. Dimethyl sulfoxide and water extracts of propolis of 20 μg/mL reduced the cell viability to 24.5% and 17.7%, respectively. Statistically significant discriminatory peaks between control PC-3 cells and dimethyl sulfoxide extract of propolis-treated PC-3 cells were found to be the proteomic features at m/z 5143, 8703, 12661, 20184 and 32794, detected by CM10 ProteinChip, and the peak at m/z 3772, detected by Q10 ProteinChip. Between control PC-3 cells and water extract of propolis-treated PC-3 cells, statistically significant discriminatory peaks were found to be the proteomic features at m/z 15846, 16052 and 24658, detected by CM10 ProteinChip and the peaks at m/z 10348, 10899 and 11603, detected by Q10 ProteinChip.ConclusionsIt was concluded that dimethyl sulfoxide and water extracts of Turkish propolis may have anti-proliferative activity through differentiating protein expression profile in PC-3 prostate cancer cell lines along with their antioxidant capacity.

Application of serum proteomic mass spectrum analysis in breast cancer

To analyze the characteristics of serum proteins mass spectra in healthy controls, benign breast tumors, and CA15-3 negative or CA15-3 positive breast cancer patients by surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS). Tissue samples of 113 cases of breast cancer (93 case of CA15-3 negative, 20 case of CA15-3 positive), 103 cases of benign breast tumor and 92 cases of healthy controls were examined and analyzed by SELDI and protein chip (CM10) techniques. Biomarker Pattern Software (BPS) was used to detect the protein peaks significantly different between them and establish a diagnostic pattern which was further evaluated by a blind test. Twelve significantly different protein peaks were found in serum samples between breast cancer patients and healthy controls. Eleven significantly different peaks were found between benign breast tumor patients and healthy controls. By combined analysis of those three different protein mass spectra, the peak 15 952 was found to be significantly different between breast cancer group and healthy controls, and the peak 7985 was significantly different among breast cancer group, benign breast tumor group and health controls. The blind test with the differential proteins for the serum samples of 93 cases of CA15-3 negative breast cancer and 36 cases of benign breast tumors showed that the sensitivity was 80.6% and specificity was 91.7%. The blind test in 20 cases of CA15-3 positive breast cancer and 36 cases of benign breast tumors showed that the sensitivity was 75.0% and specificity was 91.7%. Four significantly different protein peaks were found between the benign breast tumor patients and CA15-3 negative breast cancer patients. No significantly different protein were found between CA15-3 negative and CA15-3 positive patients. Significantly different protein peaks can be screened out in breast cancer, benign breast tumor patients and healthy controls by SELDI-TOF-MS analysis.

Proteomic investigations of the ventriculo-lumbar gradient in human CSF

Cerebrospinal fluid (CSF) is an ideal biological material in which to search for new biomarkers for improved diagnosis of neurological diseases. During a lumbar puncture between 5 and 15 mL of CSF are obtained. Previous studies have assessed the ventriculo-lumbar concentration gradient of a number of specific proteins. In the present study we took a proteomics approach to investigate the possible concentration gradient of a panel of proteins and peptides in the CSF of 16 patients with neurodegenerative diseases. Using two different mass spectrometry techniques, matrix assisted laser desorption ionization time of flight (MALDI-TOF) and surface enhanced laser desorption ionization time of flight (SELDI-TOF), we found that only one of the investigated proteins, apolipoprotein CI, was significantly decreased between the 1st and the 10th mL of CSF. Furthermore, we confirmed previous results showing a significant decrease in albumin concentration from the first to the last CSF aliquots. In conclusion, we found a significant gradient effect for only two of the measured proteins. However, a standardized procedure for CSF collection for diagnostic and research purposes is crucial to allow comparisons of results between patient groups and between laboratories. This is especially important since CSF is usually collected at several centres and variation in sampled CSF due to pre-analytical factors could complicate the interpretation of the results.

The screening and identification of Apolipoprotein A-II from serum differential proteins in hepatocellular carcinoma patients

To screen differential proteins in serum from hepatocellular carcinoma (HCC) patients by Proteomic Technology and to purify and identify them. Surface enhanced laser desorption Ionization time of flight-mass spectrum (SELDI-TOF-MS) was employed to screen differential proteins in serum from 33 HCC patients and 33 control cases, and then to purify and identify them using isoelectric precipitation, Tricine sodium dodecyl sulphate polyacrylamide gel electrophoresis (Tricine-SDS-PAGE) and high performance liquid chromatography tandem Mass Spectrum (HPLC-MS). 65 protein peaks in the range of relative molecular weight from 2,000 to 10,000 were found significant difference (P less than 0.05) between the patient group and control group. Based on these differential protein peaks, diagnostic model for HCC detection was established and its sensitivity and specificity were 100% and 96.97% respectively. Proteins with 8,706.5 and 8,579.2 relative molecular weights (the t value was 2.562 and 2.783 respectively, and P value was 0.013 and 0.015 respectively) out of the 65 differential proteins were purified and identified, and then recognized as Apolipoprotein AII (Apo AII). Apo AII is probably a differential protein of HCC and maybe related to the pathogenesis of HCC.

Blood-Borne Amyloid-β Dimer Correlates with Clinical Markers of Alzheimer's Disease

Alzheimer's disease (AD) is the most common age-related dementia. Unfortunately due to a lack of validated biomarkers definitive diagnosis relies on the histological demonstration of amyloid-beta (Abeta) plaques and tau neurofibrillary tangles. Abeta processing is implicated in AD progression and many therapeutic strategies target various aspects of this biology. While Abeta deposition is the most prominent feature of AD, oligomeric forms of Abeta have been implicated as the toxic species inducing the neuronal dysfunction. Currently there are no methods allowing routine monitoring of levels of such species in living populations. We have used surface enhanced laser desorption ionization time of flight (SELDI-TOF) mass spectrometry incorporating antibody capture to investigate whether the cellular membrane-containing fraction of blood provides a new source of biomarkers. There are significant differences in the mass spectra profiles of AD compared with HC subjects, with significantly higher levels of Abeta monomer and dimer in the blood of AD subjects. Furthermore, levels of these species correlated with clinical markers of AD including brain Abeta burden, cognitive impairment and brain atrophy. These results indicate that fundamental biochemical events relevant to AD can be monitored in blood, and that the species detected may be useful clinical biomarkers for AD.

Regulation of CXCR/IL-8 in Human Airway Epithelial Cells

Background: Severe asthma is characterized by neutrophilic inflammation and high levels of interleukin (IL)-8. Airway epithelial cells play a pivotal role in the pathogenesis and chronicity of asthma. The objective of this work was to determine whether CXC receptors were involved in human small airway epithelial cell (SAEC) activity by incubating them with IL-8; the investigation also included a proteomic approach. Methods: IL-6 and intercellular adhesion molecule-1 (ICAM-1) were assessed by ELISA and flow cytometry, respectively. CXCR-1 and CXCR-2 receptor mRNA and protein expressions were analyzed by RT-PCR, immunocytochemistry and flow cytometry. Cells were incubated with different concentrations (0–100 ng/ml) of IL-8. The involvement of both receptors was assessed using specific antibodies. Results: Only the CXCR-1 receptor was expressed in SAECs. IL-8 (50 ng/ml, 12 h) induced the release of IL-6 and had no effect on ICAM-1. Supernatants analyzed by surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF MS) showed very weak differences in peptide profiles. Interestingly, 4,820-m/z peptide release was detected in the presence of IL-8 and abolished by CXCR-1 antibody. Discussion: The present study illustrated the fact that IL-8 mediated by CXCR-1 increased IL-6. We also highlight the usefulness of SELDI ProteinChip technology to confirm the potential variation of peptide profile. Moreover, we were able to detect the 4,820-m/z peptide secreted in vitro by human airway epithelial cells induced by IL-8 via CXCR-1 receptor. Determination of the protein secretion profile in response to inflammatory stimuli could be an important therapeutic strategy in severe asthma.

Application of saliva protein fingerprints in the diagnosis of oral squamous cell cancer by surface enhanced laser desorption ionization time of flight mass

To screen proteomic markers of oral precancerous lesion, local and metastatic squamous cell cancer from human saliva. Seventeen patients with oral squamous cell carcinoma, six cases with leukoplakia, seven cases with local metastasis and 15 healthy subjects were selected. All patients were diagnosed of T(1)N(0)M(0) and did not accept any preoperative treatment. Saliva samples were collected preoperatively, combined in the chips (CM-10) for two copies, and tested by surface enhanced laser desorption/ionization (SELDI) mass spectrometry respectively. Chips were detected by the PBS-II plus mass spectrometer reader. Mass accuracy was calibrated by the all-in-one peptide molecular mass standard (ciphergen ciosystems). The differentiated pattern between oral squamous cell carcinoma and healthy people consisted of four biomarker peaks of 5797, 2902, 3883, 4951 (mass/charge) with the sensitivity of 88.24% and specificity of 93.33%. The differentiated pattern between oral squamous cell carcinoma and leukoplakia consisted of three biomarker peaks of 5818, 4617 and 3884 with the sensitivity of 100.00% and specificity of 100.00%. The differentiated pattern between oral squamous cell carcinoma and oral cancer with local metastatic consisted of three biomarker peaks of 55 809 and 5383 (mass/charge) with the sensitivity of 94.12% and specificity of 85.71%. The biomarkers selected by SELDI could help in the adjuvant early diagnosis of oral cancer and forecasting the transformation from leukoplakia to oral cancer and metastasis.

Rapid identification of Staphylococcus aureus by surface enhanced laser desorption and ionization time of flight mass spectrometry

Staphylococcus aureus ( S. aureus), a vital nosocomial pathogen, is responsible for several diseases. With the increasing isolation rate in clinical specimens, rapid identification of this bacterial species is required. But present identification via conventional methods is time-consuming and lacks accuracy. The purpose of the current study was to evaluate the use of surface enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF MS) for rapid identification of S. aureus. A total of 120 clinical isolates of S. aureus and 153 non- S. aureus species were identified by conventional methods, and the species nature of all staphylococci was further confirmed by 16S rDNA sequencing. All strains observed were analyzed by SELDI-TOF MS. An identification model for S. aureus was developed and validated by an artificial neural network. The model based on 6 protein peaks exhibited a sensitivity of 98.4% and specificity of 98.6%. This strategy has the potential for rapid identification of S. aureus.

High resolution preparation of monocyte-derived macrophages (MDM) protein fractions for clinical proteomics.

BackgroundMacrophages are involved in a number of key physiological processes and complex responses such as inflammatory, immunological, infectious diseases and iron homeostasis. These cells are specialised for iron storage and recycling from senescent erythrocytes so they play a central role in the fine tuning of iron balancing and distribution. The comprehension of the many physiological responses of macrophages implies the study of the related molecular events. To this regard, proteomic analysis, is one of the most powerful tools for the elucidation of the molecular mechanisms, in terms of changes in protein expression levels.ResultsOur aim was to optimize a protocol for protein fractionation and high resolution mapping using human macrophages for clinical studies. We exploited a fractionation protocol based on the neutral detergent Triton X-114. The 2D maps of the fractions obtained showed high resolution and a good level of purity. Western immunoblotting and mass spectrometry (MS/MS analysis) indicated no fraction cross contamination. On 2D-PAGE mini gels (7 × 8 cm) we could count more than five hundred protein spots, substantially increasing the resolution and the number of detectable proteins for the macrophage proteome. The fractions were also evaluated, with preliminary experiments, using Surface Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS).ConclusionThis relatively simple method allows deep investigation into macrophages proteomics producing discrete and accurate protein fractions, especially membrane-associated and integral proteins. The adapted protocol seems highly suitable for further studies of clinical proteomics, especially for the elucidation of the molecular mechanisms controlling iron homeostasis in normal and disease conditions.

Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS

The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species.

Proteomic Diagnosis Models from Serum for Early Detection of Oral Squamous Cell Carcinoma

The early diagnosis of oral squamous cell carcinoma (OSCC) is crucial to prevent deformity and malfunction post-surgery, as well as to allow clinicians to make a rapid decision about treatment. The aim of this study was to search a serum diagnostic model at a molecular level for OSCC. After collection and processing of serum from 28 OSCC patients and 32 healthy volunteers in the Department of Stomatology at the university hospital, samples were detected using Surface Enhanced Laser Desorption Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS) technology with CM10 protein chip and bioinformatics. Seven protein mass peaks were screened out to build a serum diagnosis model with a significant P value, respectively, and the sensitivity, specificity, and total accuracy were 93.75%, 92.86%, and 93.33%. The use of serum protein fingerprint provides a promising approach for early diagnostics, which could benefit determining preventative and therapeutic stages of patients with OSCC.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment

The signature for human immunodeficiency virus type 1 (HIV-1) neurovirulence remains a subject of intense debate. Macrophage viral tropism is one prerequisite but others, including virus-induced alterations in innate and adaptive immunity, remain under investigation. HIV-1-infected mononuclear phagocytes (MPs; perivascular macrophages and microglia) secrete toxins that affect neurons. The authors hypothesize that neurovirulent HIV-1 variants affect the MP proteome by inducing a signature of neurotoxic proteins and thus affect cognitive function. To test this hypothesis, HIV-1 isolates obtained from peripheral blood of women with normal cognition (NC) were compared to isolates obtained from women with cognitive impairment (CI) and to the laboratory adapted SF162, a spinal fluid R5 isolate from a patient with HIV-1-associated dementia. HIV-1 isolates were used to infect monocyte-derived macrophages (MDMs) and infection monitored by secreted HIV-1 p24 by enzyme-linked immunosorbent assay (ELISA). Cell lysates of uninfected and HIV-1-infected MDMs at 14 days post infection were fractionated by cationic exchange chromatography and analyzed by surface enhanced laser desorption ionization time of flight (SELDI-TOF) using generalized estimating equations statistics. Proteins were separated by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1D SDS-PAGE) and identified by tandem mass spectrometry. Levels of viral replication were similar amongst the HIV-1 isolates, although higher levels were obtained from one viral strain obtained from a patient with CI. Significant differences were found in protein profiles between virus-infected MDMs with NC, CI, and SF162 isolates (adjusted P value after multiple testing corrections, or q value <.10). The authors identified 6 unique proteins in NC, 7 in SF162, and 20 in CI. Three proteins were common to SF162 and CI strains. The MDM proteins linked to infection with CI strains were related to apoptosis, chemotaxis, inflammation, and redox metabolism. These findings support the hypothesis that the macrophage proteome differ when infected with viral isolates of women with and without CI.

Biomarkers for cystic fibrosis lung disease: Application of SELDI-TOF mass spectrometry to BAL fluid

Background For cystic fibrosis (CF) patients there is a lack of good assays of disease activity and response to new therapeutic interventions, including gene therapy. Current measures of airways inflammation severity are insensitive or non-specific. Methods Bronchoalveolar lavage fluid from 39 CF children and 38 respiratory disease controls was obtained at bronchoscopy and analysed by surface enhanced laser desorption ionisation time of flight (SELDI-TOF) mass spectrometry. Recognized proteins were assessed for CF disease specificity. Individual protein identification of specific peaks was performed. Results 1277 proteins/peptides, > 4 kDa, were detected using 12 different surfaces and binding conditions. 202 proteins/peptides were differentially expressed in the CF samples ( p < 0.001), 167 up-regulated and 35 down-regulated. The most discriminatory biomarker had a mass of 5.163 kDa. The most abundant, with a mass of 10.6 kDa, was identified as s100 A8 (calgranulin A). Conclusions The application of SELDI-TOF mass spectrometry allows evaluation of proteins in BAL fluid avoiding the limitations of only analysing predetermined proteins and potentially identifying proteins not previously appreciated as biomarkers. Its application to cystic fibrosis should enable appropriate evaluation of evolving illness, of gene therapy and other new therapies.