In-depth protein characterization by mass spectrometry.

Within this chapter, various techniques and instructions for characterizing primary structure of proteins are presented, whereas the focus lies on obtaining as much complete sequence information of single proteins as possible. Especially, in the area of protein production, mass spectrometry-based detailed protein characterization plays an increasing important role for quality control. In comparison to typical proteomics applications, wherein it is mostly sufficient to identify proteins by few peptides, several complementary techniques have to be applied to maximize primary structure information and analysis steps have to be specifically adopted.

An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.

One of the major challenges for large scale proteomics research is the quality evaluation of results. Protein identification from complex biological samples or experimental setups is often a manual and subjective task which lacks profound statistical evaluation. This is not feasible for high-throughput proteomic experiments which result in large datasets of thousands of peptides and proteins and their corresponding mass spectra.

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project.

The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.

Within the pilot phase of the HUPO Brain Proteome Project, nine participating laboratories analysed human (epilepsy and/or post mortem material) and mouse brain samples (embryonic, juvenile and adult), respectively, using a variety of different state of the art techniques. Thirty-seven different analytical approaches were accomplished. Of these analyses, 17 were done differentially, i.

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.

The HUPO Brain Proteome Project is an initiative coordinating proteomics studies to characterise human and mouse brain proteomes. Proteins identified in human brain samples during the project's pilot phase were put into biological context through integration with various annotation sources followed by a bioinformatics analysis. The data set was related to the genome sequence via the genes encoding identified proteins including an assessment of splice variant identification as well as an analysis of tissue specificity of the respective transcripts.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts.

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On January 9-11, 2006 the members as well as invited analysts came together at the European Bioinformatics Institute in Hinxton, UK for the pilot studies jamboree. The results of the reprocessing were presented and tasks forces were initiated to compile, to interpret and to summarise the data obtained.

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

Towards data management of the HUPO Human Brain Proteome Project pilot phase.

The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation has just been started. In two pilot studies, 18 different laboratories are analyzing mouse brains of three age stages and human brain autopsy versus biopsy material, respectively. The overall aim is to elucidate the portfolio of available techniques as well as to elaborate common standards.

Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data.

In this work, the commonly used algorithms for mass spectrometry based protein identification, Mascot, MS-Fit, ProFound and SEQUEST, were studied in respect to the selectivity and sensitivity of their searches. The influence of various search parameters were also investigated. Approximately 6600 searches were performed using different search engines with several search parameters to establish a statistical basis.

A randomized double-blind trial of oral L-arginine for treatment of interstitial cystitis.

Purpose: Nitric oxide synthase activity is decreased in the urine of patients with interstitial cystitis compared to the urine of controls. In a preliminary trial oral L-arginine, the substrate for nitric oxide synthase, increased urinary nitric oxide synthase activity and improved interstitial cystitis symptoms. This randomized, double-blind, placebo controlled study further investigates the efficacy of L-arginine treatment for interstitial cystitis.

A monoclonal Ro-antibody and the serum of a Ro-positive patient with subacute cutaneous lupus erythematosus (SCLE) react with basal layers of human epidermis.

Skin lesions, especially at areas exposed to sunlight, prove to be a major form of manifestation of diseases related to Ro-antibodies and neonatal-, 'ANA-negative-', and cutaneous types of lupus erythematosus. A monoclonal Ro-antibody established by our group reacts with a 60 kD polypeptide in extracts from human spleen, whereas in extracts from human epidermis the monoclonal Ro-antibody and a purified Ro-antibody from a monospecific serum of a patient with subacute cutaneous lupus erythematosus reacted with a 60 kD and a 48 kD protein. Performing immunofluorescence microscopy on HEp2-cells both antibodies showed a nuclear speckled staining pattern and a reaction with cytokeratin filaments.

[Further information on the alkali resistance test].

In 90 patients the alkali resistance (AR) according to Burckhardt was measured on the back of the hand and on the thigh. Subjects with healthy skin (n = 30) reacted in a normal way. Those with healed hand eczema (n = 30) had a diminished AR in both areas tested; subjects with atopic eczema (n = 30) presented an even more diminished AR.

[Functional Fc receptor defect of granulocytes in a patient with Sjögren's syndrome].

A patient with Sjögren's syndrome exhibited markedly impaired stimulation of her granulocytes via Fc-receptors (FcR), four other stimuli elicited a normal chemiluminescent response. Unexpectedly, granulocytes of the control bore 39,000, of the patient, however, 86,000 FcR/granulocyte.

Functional Fc-receptor defect of polymorphonuclear leukocytes in a patient with Sjögren's syndrome.

We investigated polymorphonuclear leukocyte (PMN) function in a 50-year-old woman with primary Sjögren's syndrome (SS). The respiratory burst of PMN was monitored by luminol-enhanced chemiluminescence using zymosan, opsonized zymosan, zymosan-activated serum, and phorbol-myristate-acetate, as well as serial dilutions of aggregated immunoglobulin (aggIg) as Fc-receptor (FcR) stimulus. The effects of serum on the chemiluminescent response as well as the binding of aggIg to PMN were also compared.

[Highly differentiated squamous cell carcinoma of the shoulder with perineural invasion].

A de novo carcinoma of only a few weeks' duration is reported in a 34-year-old man. Histological findings revealed a well-differentiated squamous cell carcinoma with unexpected early spread deep in the dermis and subcutis and a striking affinity to the neural structures.

[Simultaneous occurrence of lupus erythematosus and hepatic porphyria--coincidence or chance association?].

We report on two cases of coexisting lupus erythematosus and hepatic porphyria and give a review of the corresponding literature. It is not clear yet, if the coincidence is accidental or if there exist any unknown relationship. 29 patients with these two conditions were found in the literature.

[Undifferentiated cutaneous angiosarcoma of the head: identification by the endothelial marker Ulex europaeus agglutinin I].

Cutaneous angiosarcoma of the head is a rare tumor of the elderly and can occur in an undifferentiated form without any clinical or histological signs of the vascular origin of this tumor. In these cases, the tumor can be identified by using endothelial cell markers, such as factor-VIII-related antigen and ulex europaeus agglutinin I, in an immunofluorescence technique or a peroxidase-antiperoxidase method. A 78-year-old patient is described who died within 18 months from such a tumor, which was diagnosed using the endothelial cell marker, ulex europaeus agglutinin I.

[Morphologic knowledge of polyneuropathy in progressive scleroderma].

The occurrence of polyneuropathy in connection with systemic sclerosis is extremely rare. Proliferative changes leading to mechanical compression of the nerves have been ascribed to an etiological involvement. In the case reported here, polyneuropathy could be verified morphologically (nervebiopsy).

[Visible hypertrophy of the musculus corrugator supercilii].

A patient with constant intumescences of the forehead due to bilateral hypertrophy of mimic muscles is reported.