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Severe COVID-19 infections increase the risk of thrombotic events and Intensive Care Units reported increased extracorporeal circuit clotting (ECC) in COVID-19 patients with acute kidney injury. We wished to determine whether hemodialysis (HD) patients with COVID-19 also have increased risk of circuit clotting.We reviewed coagulation studies and HD records, 4 weeks before and after COVID-19 polymerase chain reaction detection in HD patients between April 2020 and June 2021.Sixty-eight (33.5%) of 203 HD patients with COVID-19, 65% male, mean age 64.9 ± 15.3 years, experienced some circuit clotting, and no clotting recorded prior to positive test results. In those who experienced ECC, prothrombin, activated partial thromboplastin or thrombin times were not different, whereas median factor VIII (273 [168-419] vs. 166 [139-225] IU/dl, p 0.001), D-dimers (2654 [1381-6019] vs. 1351 [786-2334] ng/ml, p 0.05), and fibrinogen (5.6 ± 1.4 vs. 4.9 ± 1.4 g/L, p 0.05) were greater. Antithrombin (94 [83-112] vs. 89 [84-103] IU/dl), protein C (102 [80-130] vs. 86 [76-106] IU/dl), protein S (65 [61-75] vs. 65 [52-79] IU/dl) and platelet counts (193 [138-243] vs. 174 [138-229] × 10Extracorporeal circuit clotting was increased within 4 weeks of testing positive for COVID-19. Clotting was associated with increased factor VIII, fibrinogen and D-dimer, suggesting that the risk of circuit clotting was related to the inflammatory response to COVID-19.

Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the susceptibility for recurrent AKI or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury, and the contralateral kidneys remained uninjured to enable comparison and assess injury-induced changes in the kidney proteome. A fast-acquisition rate ZenoTOF 7600 mass spectrometer was introduced for data-independent acquisition (DIA) for comprehensive protein identification and quantification. Short microflow gradients and the generation of a deep kidney-specific spectral library allowed for high-throughput, comprehensive protein quantification. Upon AKI, the kidney proteome was completely remodeled, and over half of the 3,945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins that function in fatty acid oxidation, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured mice exhibited severely declined health. The comprehensive and sensitive kidney-specific DIA assays highlighted here feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome and will serve as useful tools for developing novel therapeutics to remediate kidney function.

We established a robust capillary-flow data-independent acquisition MS platform capable of measuring 31 plasma proteomes per day without the need of repeated acquisition of the same sample. We acquired 1508 samples of the DiOGenes study (multicentered, Europa-wide caloric restriction weight loss and maintenance study of overweight and obese, non-diabetic participants). This was achieved using a single analytical column. Comprehensive biological reactions to weight loss and maintenance were observed., Graphical Abstract Highlights Robust capillary-flow DIA was established at 31 clinical samples per day. 1508 samples of dietary intervention study DiOGenes were measured on a single column. Comprehensive biological reactions to weight loss and maintenance were observed. Comparison to independent studies shows high reproducibility of potential biomarkers., Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%. The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA. In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.

Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post‐translational turnover, we devised a strategy combining pulse stable isotope‐labeled amino acids in cells (pSILAC), data‐independent acquisition mass spectrometry (DIA‐MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome‐wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation., Molecular Systems Biology, 16 (3), ISSN:1744-4292

Growing public awareness about the state of the environment, chemical product safety and new chemical regulatory policies is driving demand for leaders who are able to understand the science underlying environmental challenges and develop innovative solutions. Chalcones belong to the flavonoid family and display several pharmacological activities which are very important. They can be used as an initial compound for synthesis of a lot of compounds. In this research chalcone derivative are made via green chemistry route and analysed their physical and antimicrobial activity.

Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence. 7739 proteins were identified in mouse tissues using 2-or-more peptides/protein and 8121 when including the 382 proteins that were identified based on a single peptide sequence. Missing values for proteins were within 0.3 to 2.1% and median coefficients of variation of 4.7 to 6.2% among technical triplicates. In very complex mixtures, we could quantify 10,780 proteins and 12,192 proteins when including the 1412 proteins that were identified based on a single peptide sequence. Using this optimized DIA, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1-barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability.

© 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license Background: The Lancet Commission on Global Surgery established the Three Delays framework, categorising delays in accessing timely surgical care into delays in seeking care (First Delay), reaching care (Second Delay), and receiving care (Third Delay). Globally, knowledge gaps regarding delays for fracture care, and the lack of large prospective studies informed the rationale for our international observational study. We investigated delays in hospital admission as a surrogate for accessing timely fracture care and explored factors associated with delayed hospital admission. Methods: In this prospective observational substudy of the ongoing International Orthopaedic Multicenter Study in Fracture Care (INORMUS), we enrolled patients with fracture across 49 hospitals in 18 low-income and middle-income countries, categorised into the regions of China, Africa, India, south and east Asia, and Latin America. Eligible patients were aged 18 years or older and had been admitted to a hospital within 3 months of sustaining an orthopaedic trauma. We collected demographic injury data and time to hospital admission. Our primary outcome was the number of patients with open and closed fractures who were delayed in their admission to a treating hospital. Delays for patients with open fractures were defined as being more than 2 h from the time of injury (in accordance with the Lancet Commission on Global Surgery) and for those with closed fractures as being a delay of more than 24 h. Secondary outcomes were reasons for delay for all patients with either open or closed fractures who were delayed for more than 24 h. We did logistic regression analyses to identify risk factors of delays of more than 2 h in patients with open fractures and delays of more than 24 h in patients with closed fractures. Logistic regressions were adjusted for region, age, employment, urban living, health insurance, interfacility referral, method of transportation, number of fractures, mechanism of injury, and fracture location. We further calculated adjusted relative risk (RR) from adjusted odds ratios, adjusted for the same variables. This study was registered with ClinicalTrials.gov, NCT02150980, and is ongoing. Findings: Between April 3, 2014, and May 10, 2019, we enrolled 31 255 patients with fractures, with a median age of 45 years (IQR 31–62), of whom 19 937 (63·8%) were men, and 14 524 (46·5%) had lower limb fractures, making them the most common fractures. Of 5256 patients with open fractures, 3778 (71·9%) were not admitted to hospital within 2 h. Of 25 999 patients with closed fractures, 7141 (27·5%) were delayed by more than 24 h. Of all regions, Latin America had the greatest proportions of patients with delays (173 [88·7%] of 195 patients with open fractures; 426 [44·7%] of 952 with closed fractures). Among patients delayed by more than 24 h, the most common reason for delays were interfacility referrals (3755 [47·7%] of 7875) and Third Delays (cumulatively interfacility referral and delay in emergency department: 3974 [50·5%]), while Second Delays (delays in reaching care) were the least common (423 [5·4%]). Compared with other methods of transportation (eg, walking, rickshaw), ambulances led to delay in transporting patients with open fractures to a treating hospital (adjusted RR 0·66, 99% CI 0·46–0·93). Compared with patients with closed lower limb fractures, patients with closed spine (adjusted RR 2·47, 99% CI 2·17–2·81) and pelvic (1·35, 1·10–1·66) fractures were most likely to have delays of more than 24 h before admission to hospital. Interpretation: In low-income and middle-income countries, timely hospital admission remains largely inaccessible, especially among patients with open fractures. Reducing hospital-based delays in receiving care, and, in particular, improving interfacility referral systems are the most substantial tools for reducing delays in admissions to hospital. Funding: National Health and Medical Research Council of Australia, Canadian Institutes of Health Research, McMaster Surgical Associates, and Hamilton Health Sciences.

Introduction Laboratory monitoring for factor VIII inhibitors ideally requires samples with the lowest possible factor VIII (FVIII) level, potentially challenging in patients with congenital haemophilia A (CHA) receiving regular prophylaxis and acquired haemophilia A (AHA) patients with endogenous FVIII. Inactivation of FVIII by preheating (preheat treatment, PHT) of patient plasma has been suggested to facilitate monitoring. Aim To evaluate the clinical utility of PHT prior to inhibitor analysis by modified Nijmegen-Bethesda assay (mNBA) in patients with CHA and AHA. Methods Inhibitor screening by mNBA under standard conditions and with PHT at 56°C for 30, 60 and 90 minutes was evaluated. FVIII inhibitor results between 2007 and 2010 without PHT (720 results from 222 CHA and AHA patients), and between 2011 and 2014 post-PHT (1102 results from 302 patients) were available for analysis. Results Of total 1822 results available, 61% were from severe HA patients, 22% from mild and moderate HA and 16% from AHA. Pre-PHT, 74% of samples were analysed by the mNBA, and the remaining 26% were not tested as FVIII levels were >20 IU/dL as per local protocol. Postintroduction of PHT (90 and 60 minutes), 96% of samples received were analysed for an inhibitor. Post-PHT in patients with AHA (n = 26), 69% of samples tested with factor VIII levels >20 IU/dL were found to have detectable inhibitor. Conclusion FVIII inhibitor testing using PHT at 56°C for 60 minutes facilitates inhibitor surveillance of CHA on prophylaxis. Potentially, 30 minutes at 56°C might be equally efficacious. In AHA receiving immunosuppression, monitoring of inhibitor titre after initial factor VIII response might enable personalized immunosuppression.

Comprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances have been made in recent years, full proteome coverage for complex samples remains challenging due to the high dynamic range of protein expression. Additionally, when studying disease regulatory proteins, biomarkers or potential drug targets are often low abundant, such as for instance kinases and transcription factors. Here, we show that with improvements in chromatography and data analysis the single shot proteome coverage can go beyond 10 000 proteins in human tissue. In a testis cancer study, we quantified 11 200 proteins using data independent acquisition (DIA). This depth was achieved with a false discovery rate of 1% which was experimentally validated using a two species test. We introduce the concept of hybrid libraries which combines the strength of direct searching of DIA data as well as the use of large project-specific or published DDA data sets. Remarkably deep proteome coverage is possible using hybrid libraries without the additional burden of creating a project-specific library. Within the testis cancer set, we found a large proportion of proteins in an altered expression (in total: 3351; 1453 increased in cancer). Many of these proteins could be linked to the hallmarks of cancer. For example, the complement system was downregulated which helps to evade the immune response and chromosomal replication was upregulated indicating a dysregulated cell cycle.

In this paper, we construct explicit families of quantum error correcting codes based on cyclic codes. But for a crucial theoretical idea that we introduce here, namely working with a modified symplectic form as the basis of Weyl commutation, these codes would not have been possible — under the standard symplectic form, there are Galois theoretic no-go theorems on cyclic codes [7], [Corollary IV.5, page 651], [6], [Corollary 5.16, page 51] of certain lengths. More importantly, we circumvent the above no-go theorems without disturbing the one crucial property that cyclic codes have — efficient decoding algorithms. Recall that for general codes, efficient decoding algorithms do not exist if some widely believed complexity theoretic assumptions are true hence this is a crucial property to have. Cyclicity is a basis dependent property and for codes that we construct, is only evident in the modified symplectic setting. If we were to recast this code using the standard symplectic form, there would be a basis change on the underlying vector space that disturbs cyclicity. Hence, this change of perspective that we have here is crucial not only in the construction, where we had to circumvent the no-go theorems that we mentioned above, but also in the design of efficient decoding algorithm. Theoretically our result is also tight: we have a complete characterization (Theorem 6) of the codes that we construct here.

Targeted analysis of data-independent acquisition (DIA) data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted retention time (RT). RTs, however, are not comparable on an absolute scale, especially if heterogeneous measurements are combined. Here, we present a method for high-precision prediction of RT, which significantly improves the quality of targeted DIA analysis compared to in silico RT prediction and the state of the art indexed retention time (iRT) normalization approach. We describe a high-precision normalized RT algorithm, which is implemented in the Spectronaut software. We, furthermore, investigate the influence of nine different experimental factors, such as chromatographic mobile and stationary phase, on iRT precision. In summary, we show that using targeted analysis of DIA data with high-precision iRT significantly increases sensitivity and data quality. The iRT values are generally transferable across a wide range of experimental conditions. Best results, however, are achieved if library generation and analytical measurements are performed on the same system.

Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled the cataloging of thousands of sites throughout the cell; however, identifying regulatory acetylation marks have proven to be a daunting task. Knowledge of the kinetics and stoichiometry of site-specific acetylation is an important factor to uncover function. Here, an improved method of quantifying acetylation stoichiometry was developed and validated, providing a detailed landscape of dynamic acetylation stoichiometry within cellular compartments. The dynamic nature of site-specific acetylation in response to serum stimulation was revealed. In two distinct human cell lines, growth factor stimulation led to site-specific, temporal acetylation changes, revealing diverse kinetic profiles that clustered into several groups. Overlap of dynamic acetylation sites among two different human cell lines suggested similar regulatory control points across major cellular pathways that include splicing, translation, and protein homeostasis. Rapid increases in acetylation on protein translational machinery suggest a positive regulatory role under progrowth conditions. Finally, higher median stoichiometry was observed in cellular compartments where active acetyltransferases are well described. Data sets can be accessed through ProteomExchange via the MassIVE repository (ProteomExchange: PXD014453; MassIVE: MSV000084029).

The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)1 treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling., Molecular & Cellular Proteomics, 14 (5), ISSN:1535-9476, ISSN:1535-9484

Background— Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. Methods and Results— Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS ( Conclusions— The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.

LC-MALDI provides an often overlooked opportunity to exploit the separation between LC-MS and MS/MS stages of a 2D-LC-MS-based proteomics experiment, that is, by making a smarter selection for precursor fragmentation. Apex Peptide Elution Chain Selection (APECS) is a simple and powerful method for intensity-based peptide selection in a complex sample separated by 2D-LC, using a MALDI-TOF/TOF instrument. It removes the peptide redundancy present in the adjacent first-dimension (typically strong cation exchange, SCX) fractions by constructing peptide elution profiles that link the precursor ions of the same peptide across SCX fractions. Subsequently, the precursor ion most likely to fragment successfully in a given profile is selected for fragmentation analysis, selecting on precursor intensity and absence of adjacent ions that may cofragment. To make the method independent of experiment-specific tolerance criteria, we introduce the concept of the branching factor, which measures the likelihood of false clustering of precursor ions based on past experiments. By validation with a complex proteome sample of Arabidopsis thaliana, APECS identified an equivalent number of peptides as a conventional data-dependent acquisition method but with a 35% smaller work load. Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides.

Transport of solutes between the cytosol and the vacuolar lumen is of crucial importance for various functions of vacuoles, including ion homeostasis; detoxification; storage of different molecules such as amino acids, phosphate, and calcium ions; and proteolysis. To identify proteins that catalyze solute transport across the vacuolar membrane, the membrane proteome of purified Saccharomyces cerevisiae vacuoles was analyzed. Subtractive proteomics was used to distinguish contaminants from true vacuolar proteins by comparing the relative abundances of proteins in pure and crude preparations. A robust statistical analysis combining enrichment ranking with the double boundary iterative group analysis revealed that 148 proteins were significantly enriched in the pure vacuolar preparations. Among these proteins were well characterized vacuolar proteins, such as the subunits of the vacuolar H(+)-ATPase, but also proteins that had not previously been assigned to a cellular location, many of which are likely novel vacuolar membrane transporters, e. g. for nucleosides and oligopeptides. Although the majority of contaminating proteins from other organelles were depleted from the pure vacuolar membranes, some proteins annotated to reside in other cellular locations were enriched along with the vacuolar proteins. In many cases the enrichment of these proteins is biologically relevant, and we discuss that a large group is involved in membrane fusion and protein trafficking to vacuoles and may have multiple localizations. Other proteins are degraded in vacuoles, and in some cases database annotations are likely to be incomplete or incorrect. Our work provides a wealth of information on vacuolar biology and a solid basis for further characterization of vacuolar functions. Molecular & Cellular Proteomics 8:380-392, 2009.

Over the last decade, a wide range of philosophies and management strategies have been embraced by an increasing number of healthcare organizations, with the principal goal of improving productivity and the quality of care while reducing the associated costs. These have had a significant impact on various healthcare services, including the delivery of surgical care. These philosophies and strategies are composed of scientific techniques and methods, a majority of which can be classified under the Industrial and Systems Engineering (ISE) field of study. For the most part, these techniques have proved to be instrumental in engineering radical changes and improvements in the ailing healthcare industry. This research seeks to contribute to the growing efforts on the application of ISE tools in the healthcare industry. First, an attempt is made to illustrate how various techniques can be used to engineer tangible benefits into the processes for surgical care delivery. Axiomatic Design (AD) concepts are leveraged to synthesize redesign changes, which are then applied to a conceptual model of the surgical system. The model is developed using a Petri Net (PN) technique and subsequently validated, verified and analyzed using PN heuristics and Dependency Structure Matrix (DSM). The outcomes of this redesign depict process improvements with the potential to enhance the quality of surgical care while enabling close to 70 % productivity gains. As a result, this research proposes a framework for the systematic redesign of processes, especially when changes need to be tested and verified before implementation. The techniques identified within this framework are ideal for the successful completion of the ‘design’ and ‘plan’ phases when pursuing operations management philosophies like Six-Sigma (SS) and Total Quality Management (TQM).

This article has been withdrawn by the authors. This article did not comply with the editorial guidelines of MCP. Specifically, single peptide based protein identifications of 9-19% were included in the analysis and discussed in the results and conclusions. We wish to withdraw this article and resubmit a clarified, corrected manuscript for review.

In this paper a measure that computes dissimilarity score is proposed that can be used to find out the distance between two face samples. Gradient Binary Pattern are applied over face samples to transform them into some robust representation. Later corner features are extracted and they are tracked using KL-tracking and the number of unsuccessfully tracked corners are counted between each testing and training images. Four publicly available face databases are used for system testing, viz. YALE, BERN, ORL, CALTECH.

The identification of proteins in proteomics experiments is usually based on mass information derived from tandem mass spectrometry data. To improve the performance of the identification algorithms, additional information available in the fragment peak intensity patterns has been shown to be useful. In this study, we consider the effect of iTRAQ labeling on the fragment peak intensity patterns of singly charged peptides from MALDI tandem MS data. The presence of an iTRAQmodified basic group on the N-terminus leads to a more pronounced set of b-ion peaks and distinct changes in the abundance of specific peptide types. We performed a simple intensity prediction by using a decision-tree machine learning approach and were able to show that the relative ion abundance in a spectrum can be correctly predicted and distinguished from closely related sequences. This information will be useful for the development of improved method-specific intensity-based protein identification algorithms.

Evaluating best strategies across the organization has been a major challenge for healthcare decision makers. The complex nature of patient flow and the unpredictability involved makes discrete event simulation an ideal tool for evaluating strategic decisions in hospital inpatient capacity planning. In this paper, simulation was used to evaluate scenarios pertaining to hospital inpatient capacities. The requirement of additional capacities over the planning horizon was modeled and evaluated. Similarly, the impacts of the opening of a new competing hospital facility were studied.

Quantitative phosphoproteomics has in recent years revolutionized understanding of cell signaling, but it remains a challenge to scale the technology for high-throughput analyses. Here we present a rapid and reproducible phosphoproteomics approach to systematically analyze hundreds of samples by fast liquid chromatography tandem mass spectrometry using data independent acquisition (DIA). To overcome the inherent issue of positional phosphopeptide isomers in DIA-based phosphoproteomics, we developed and employed an accurate site localization scoring algorithm, which is incorporated into the Spectronaut software tool. Using a library of synthetic phosphopeptides spiked-in to a yeast phosphoproteome in different ratios we show that it is on par with the top site localization score for data-dependent acquisition (DDA) based phosphoproteomics. Single-shot DIA-based phosphoproteomics achieved an order of magnitude broader dynamic range, higher reproducibility of identification and improved sensitivity and accuracy of quantification compared to state-of-the-art DDA-based phosphoproteomics. Importantly, direct DIA without the need of spectral libraries performed almost on par with analyses using specific project-specific libraries. Moreover, we implemented and benchmarked an algorithm for globally determining phosphorylation site stoichiometry in DIA. Finally, we demonstrate the scalability of the DIA approach by systematically analyzing the effects of thirty different kinase inhibitors in context of epidermal growth factor (EGF) signaling showing that a large proportion of EGF-dependent phospho-regulation is mediated by a specific set of protein kinases.