Eckhard Nordhoff's research while affiliated with Ruhr-Universität Bochum and other places

... In both control (94%) and amon mutant (88%, n = 16) adults, mass peaks corresponding to AKH and AKHGK were detected (Figure 5A right), typically with a decreased signal-to-noise ratio for the AKH and AKHGK peaks in amon mutants. While this decreased signal-to-noise ratio indicated a lower amount of AKH and AKHGK in amon mutant CC, it is problematic to use MALDI-TOF signals per se to quantify peptides mainly due to non-homogenous analyte distribution in the co-crystallite and ion suppression effects (see [46,47]). A solution to minimize these adverse effect is a proper choice of matrix, decomplexing of the sample and the application of chemically similar internal standards (see [46,47] ). ...

... which is based on the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) primer extension assay, was used to genotype three SNPs (rs4836317, rs9327438 and rs6866678) 54 . We used the iPlex genotyping assay, which showed increased plexing efficiency and flexibility for the MassARRAY system via single base primer extension with mass-modified terminators 55 . All primers were designed according to the sequence of the forward strand from the dbSNP database (http://www.ncbi.nlm.nih.gov/SNP/). ...

... Hence, the FDR is more error-prone in case of mixed host-pathogen samples where two organisms are combined. One of the most suitable methods to bypass this limitation is the so-called spectra-to-spectra search [26]. Here the number of database entries is significantly reduced. ...

... PCNSL represents a specific extranodal subtype of DLBCL with molecular similarities to systemic DLBCL of MCD or C5 type with frequent mutations in MYD88 and CD79 (195,202). PCNSL show strong over-representation of IGVH4-34, and poly-reactivity against a plethora of antigens was reported (196,203). In addition, sterile a-motif domain containing protein 14 (SAMD14) and neural tissue-specific F-actin binding protein I (neurabin-I) with a homologous SAM domain were identified as specific auto-antigenic targets of recombinant BCRs of PCNSL and SAMD14/neurabin-I specific autoantibodies were detected in sera and cerebrospinal fluid of patients. ...

... Modification with macromolecule materials increases aptamers' molecular weight. For example, Andres Jaschke JPF et al. demonstrated that aptamers modified with 20 kDa polyethylene glycol (PEG) moiety had lower renal excretion rate and ideal tissue distribution and the half-life in vivo was also increased [132]. Besides, other modified strategies such as linking nanomaterials, liposomes, diacylglycerol, streptomycin, cholesterol [133] and so on are feasible for increasing molecular weight to improve the biostability [134,135]. ...

... trifluoroacetic acid (TFA) for 1 h. Sample preparation was carried out according to the dried droplet method [24] using sinapinic acid (SA) as matrix, which was prepared by dissolving SA in ACN/H 2 O (50:50, v/v) with 0.05% (v/v) TFA at a concentration of 10 mg/ml. Sample/matrix solution mixture (1:14, v/v) of 2 l was deposited onto a 100-sample MALDI probe tip and dried at room temperature. ...

... Another way to combine SPR with MALDI MS is to collect the analytes elution from the sensor chip and then perform MALDI MS analysis [19]. Moreover, the eluted analytes can also be analyzed by other ionization methods, e.g., electrospray ionization (ESI) [20]. ...

... Autoimmunity, as a pathogenic mechanism in ALS, has been initially proposed in the nineties by Appel and colleagues (23,24) who demonstrated in patients and mice the presence of specific autoantibodies against calcium channel. This hypothesis was not much examined in the following years and remained controversial even if numerous autoantibodies were recognized in ALS patients (25,26). Some recent works, including clinical evidence (27), support the view that an immune reactivity against motor nerve terminals can lead to an alteration of calcium homeostasis. ...

... The washing steps were repeated three times. Gel pieces were reconstituted in 0.025 µg/µl trypsin for 10 min, before the samples were digested in 50 mM ammonium bicarbonate overnight at 37 o C. Supernatant was treated in accordance with Gobom et al. (15). After acidification with 0.25% (v/v) trifluoracetic acid (TFA) the samples were desalted on a Downloaded from http://portlandpress.com/biochemj/article-pdf/doi/10.1042/BCJ20200559/901697/bcj-2020-0559.pdf by Copenhagen University user on 28 January 2021 custom-made micro column (plug from an Empore C18 disk (3M) and 1-2 mm Poros R2 50 µm (Thermo Scientific) in a 10 µl pipet tip). ...

... Protein concentration of the homogenate was determined densitometrically (Henkel and Bieger Fig. 1 Interactions of polyclonal antibodies directed to the Gram negative microaerophilic gastric bacterium Helicobacter pylori (α-HPy) with specific protein spots on the hEXselect multiprotein array (MPA). This array contains 23,806 spots of both full-length, and shorter protein fragments, expressed in an E. coli system, representing a total number of around 10 000 different human proteins (Büssow et al. 2000). As revealed by the green stained false color image of an X-ray film exposed to the immune incubation of a hEXselect MPA as visualized by ECL-detection, a number of pairwise immunoreactive spots revealed immunoreactivity with α-HPy, which subsequently could be identified according to their membrane location as 99 different proteins (see Table 1 for a more detailed gene description). ...