We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membrane-based proteomic sample processing method. We validated our approach on whole-cell lysate and urine and cerebrospinal fluid as clinically relevant body fluids. Without compromising peptide and protein identification, our method uses a vacuum manifold and circumvents the need for digest desalting, making our processing method compatible with standard liquid handling robots. Mass spectrometry (MS)-based proteomics is moving increasingly into the translational and clinical research arena, where robust and efficient sample processing is of particular importance. The conventional sample processing methods in proteomics, namely SDS-PAGE, or in-solution-based sample processing, are slow and laborious and thus do not easily provide the reproducibility and throughput to meet current demands. A paradigm shift was the introduction of a filteraided sample processing method (FASP), which is initially described by Manza et al.(1) and then fully realized in practice by Wisniewski et al. (2). These filter-aided methods make use of ultrafiltration membranes with molecular weight cut offs (MWCO) in the 10 to 30 kDa range to efficiently remove small molecules and salts and to capture denatured proteins on a cellulose filter even if the molecular weight of the protein is much smaller than the nominal MWCO of the ultrafiltration membrane. Thus, the denaturation step is crucial to ensure that proteins much smaller than the nominal MWCO are efficiently retained by, e.g. a 10 kDa MWCO filter.In translational and clinical proteomics, which normally include large cohorts, the multititer-well plate is the preferred format for sample processing and storage. Although the application of FASP in the 96-well plate format has been described (3, 4), the major limitation of FASP in the 96-well plate is the much slower speed at which the 96-well plates have to be centrifuged: while a single ultrafiltration unit withstands up to 14,000 ϫ g, the 96-well plate format can only be centrifuged at g-forces of up to 2,200 ϫ g. This significantly lower g-force for 96-well plates results in a slow liquid transfer, which in turn considerably prolongs the required centrifugation times to hours instead of tens of minutes for the three to four necessary centrifugation steps (i) for the initial loading, reduction and alkylation, (ii) for the different washing steps, and (iii) for the elution (3).Independent of the format FASP is performed in, the conventional FASP also requires relative large volumes of high salt concentration for efficient elution of the tryptic peptid...

Using multiplexed quantitative proteomics, we analyzed cell cycledependent changes of the human proteome. We identified >4,400 proteins, each with a six-point abundance profile across the cell cycle. Hypothesizing that proteins with similar abundance profiles are co-regulated, we clustered the proteins with abundance profiles most similar to known Anaphase-Promoting Complex/ Cyclosome (APC/C) substrates to identify additional putative APC/C substrates. This protein profile similarity screening (PPSS) analysis resulted in a shortlist enriched in kinases and kinesins. Biochemical studies on the kinesins confirmed KIFC1, KIF18A, KIF2C, and KIF4A as APC/C substrates. Furthermore, we showed that the APC/C CDH1 -dependent degradation of KIFC1 regulates the bipolar spindle formation and proper cell division. A targeted quantitative proteomics experiment showed that KIFC1 degradation is modulated by a stabilizing CDK1-dependent phosphorylation site within the degradation motif of KIFC1. The regulation of KIFC1 (de-)phosphorylation and degradation provides insights into the fidelity and proper ordering of substrate degradation by the APC/C during mitosis.

Objective Previously, we used a proteomics approach for the discovery of new diagnostic markers of acute appendicitis (AA) and identified LRG that was elevated in the urine of children with AA and enriched in diseased appendices. Here, we sought to evaluate the diagnostic utility of enzyme-linked immunoassay (ELISA) of urine LRG in a blinded, prospective, cohort study of children being evaluated for acute abdominal pain. Methods Urine LRG concentration was measured using a commercially available LRG ELISA, and selected ion monitoring (SIM) mass spectrometry (MS). Urine LRG test performance was evaluated blindly against the pathologic diagnosis and histologic grade of appendicitis. Results Urine LRG was measured in 49 patients. Mean urine LRG concentration measured using commercial LRG ELISA was significantly elevated in patients with AA, but exhibited an interference effect. Direct measurements using SIM MS demonstrated that LRG was elevated more than 100-fold in patients with AA as compared to those without, with the receiver operating characteristic area under the curve of 0.98 (95% CI = 0.96-1.0). Among patients with AA, elevations of urine LRG measured using ELISA and SIM MS correlated with the histologic severity of appendicitis. Conclusion Urine LRG ELISA allows for discrimination between patients with and without AA, but exhibits limited accuracy due to immunoassay interference. Direct measurements of urine LRG using SIM MS demonstrate superior diagnostic performance. Development of a clinical-grade urine LRG assay is needed to advance the diagnostic accuracy of clinical evaluations of appendicitis.