Asms qc Will Thompson Duke
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ASMS 2014 Analytical Core Directors Workshop. Presented by Will Thompson http://www.genome.duke.edu/cores/proteomics/contact/will-thompson/
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2) Setup is estimated to take around 20 minutes. The document recommends using the cheapest GPU option (Tesla P100) as Prosit does not heavily utilize the GPU during prediction. At least 8 CPU cores and 100GB RAM are suggested.
3) Benchmarking showed that 100,000 peptides can be predicted in 10 minutes on a Tesla P100 VM, while 1 million peptides would take around 100 minutes.
Phinney 2019 ASMS Proteome software Users group Talk
The document summarizes different methods for optimizing data-independent acquisition (DIA) workflows in a proteomics core facility. It compares the 2x green fluorescent protein (GFP) method to using a narrow chromatogram library and wide experimental window, finding the 2x GFP method works well for 2-5 samples. An example experiment profiling several proteins across conditions is described. Different permutations are tested on a subset, comparing public libraries to in-house libraries for building chromatogram libraries. The 2x GFP method using public libraries works best for depth and missing values. Challenges with ScaffoldDIA software are noted. In conclusion, DIA provides better coverage than data-dependent acquisition, especially for human samples, and can work
Genome web july 2019 presentation phinney
This document describes the work done at the UC Davis Proteomics Core Facility, which uses suspension trapping and peptide-centric DIA with deep learning to develop more universal proteomics methods. The core analyzes diverse sample types from various species using techniques like AP-MS, TMT, DIA, and PTM analysis. Peptide-centric DIA with ScaffoldDIA software provides better quantification than DDA, especially for human samples. Using Prosit deep learning to generate in silico libraries improves pathogen and protein identification from samples like infected grape sap. The core finds that DIA with gas phase fractionation works well for smaller sample sets and provides advantages over DDA for applications like undepleted serum proteomics.
Some statistical concepts relevant to proteomics data analysis
From the UC Davis Proteomics 2014 Summer Workshop
www.proteomics.ucdavis.edu
by Blythe Durbin-Johnson, Ph D.
Gene Ontology Network Enrichment Analysis
From the UC Davis Proteomics 2014 Summer Workshop
www.proteomics.ucdavis.edu
by Dmitry Grapov, Ph D
Multivariate Analysis and Visualization of Proteomic Data
From the UC Davis Proteomics 2014 Summer Workshop
www.proteomics.ucdavis.edu
by Dmitry Grapov, Ph D
Moeller proteomics course
Quantitative Proteomics presentation from our quantitative proteomics short courses at the UC Davis Genome Center Proteomics Core Facility
More from UC Davis (8)
Phinney 2019 ASMS Proteome software Users group Talk
Phinney 2019 ASMS Proteome software Users group Talk
Some statistical concepts relevant to proteomics data analysis
Some statistical concepts relevant to proteomics data analysis
Multivariate Analysis and Visualization of Proteomic Data
Multivariate Analysis and Visualization of Proteomic Data
Recently uploaded
Methods of grain storage Structures in India.pdf
•Post-harvestlossesaccountforabout10%oftotalfoodgrainsduetounscientificstorage,insects,rodents,micro-organismsetc.,
•Totalfoodgrainproductioninindiais311milliontonnesandstorageis145mt.InIndia,annualstoragelosseshavebeenestimated14mtworthofRs.7,000croreinwhichinsectsaloneaccountfornearlyRs.1,300crores.
•InIndiaoutofthetotalproduction,about30%ismarketablesurplus
•Remaining70%isretainedandstoredbyfarmersforconsumption,seed,feed.Hence,growerneedstoragefacilitytoholdaportionofproducetosellwhenthemarketingpriceisfavourable
•TradersandCo-operativesatmarketcentresneedstoragestructurestoholdgrainswhenthetransportfacilityisinadequate
快速办理(UAM毕业证书)马德里自治大学毕业证学位证一模一样
学校原件一模一样【微信：741003700 】《(UAM毕业证书)马德里自治大学毕业证学位证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
8.Isolation of pure cultures and preservation of cultures.pdf
Isolation of pure culture, its various method.
Direct Seeded Rice - Climate Smart Agriculture
Direct Seeded Rice - Climate Smart AgricultureInternational Food Policy Research Institute- South Asia Office
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
_Extraction of Ethylene oxide and 2-Chloroethanol from alternate matrices Li...
How do you know your food is safe?
Last Friday was world World Food Safety Day, facilitated by the Food and Agriculture Organization of the United Nations (FAO) and the World Health Organization (WHO) in which the slogan rightly says, 'food safety is everyone's business'. Due to this, I thought it would be worth sharing some data that I have worked on in this field!
Working at Markes International has really opened my eyes (and unfortunately my friends and family 🤣) to food safety and quality, especially with my recent application work on ethylene oxide and 2-chloroethanol residues in foodstuffs, as of the biggest global food recalls in history was and is still being implemented by the Rapid alert system for food and feed (RASFF) in 2021, for high levels of these carcinogenic compounds.
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
11.1 Role of physical biological in deterioration of grains.pdf
Storagedeteriorationisanyformoflossinquantityandqualityofbio-materials.
Themajorcausesofdeteriorationinstorage
•Physical
•Biological
•Mechanical
•Chemical
Storageonlypreservesquality.Itneverimprovesquality.
Itisadvisabletostartstoragewithqualityfoodproduct.Productwithinitialpoorqualityquicklydepreciates
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原。
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
【主营项目】
一.毕业证【q微741003700】成绩单、使馆认证、教育部认证、雅思托福成绩单、学生卡等！
二.真实使馆公证(即留学回国人员证明,不成功不收费)
三.真实教育部学历学位认证（教育部存档！教育部留服网站永久可查）
四.办理各国各大学文凭(一对一专业服务,可全程监控跟踪进度)
如果您处于以下几种情况：
◇在校期间，因各种原因未能顺利毕业……拿不到官方毕业证【q/微741003700】
◇面对父母的压力，希望尽快拿到；
◇不清楚认证流程以及材料该如何准备；
◇回国时间很长，忘记办理；
◇回国马上就要找工作，办给用人单位看；
◇企事业单位必须要求办理的
◇需要报考公务员、购买免税车、落转户口
◇申请留学生创业基金
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Music and Medieval History
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDS
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
fermented food science of sauerkraut.pptx
This ppt contains the production of a fermented food name - sauerkraut
MICROBIAL INTERACTION PPT/ MICROBIAL INTERACTION AND THEIR TYPES // PLANT MIC...
MICROBIAL INTERACTION PPT/ MICROBIAL INTERACTION AND THEIR TYPES // PLANT MIC...ABHISHEK SONI NIMT INSTITUTE OF MEDICAL AND PARAMEDCIAL SCIENCES , GOVT PG COLLEGE NOIDA
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
Recently uploaded (20)
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
_Extraction of Ethylene oxide and 2-Chloroethanol from alternate matrices Li...
_Extraction of Ethylene oxide and 2-Chloroethanol from alternate matrices Li...
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
11.1 Role of physical biological in deterioration of grains.pdf
11.1 Role of physical biological in deterioration of grains.pdf
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...
Clinical periodontology and implant dentistry 2003.pdf
Clinical periodontology and implant dentistry 2003.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
Microbiology of Central Nervous System INFECTIONS.pdf
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdf
Introduction_Ch_01_Biotech Biotechnology course .pptx
Introduction_Ch_01_Biotech Biotechnology course .pptx
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
Holsinger, Bruce W. - Music, body and desire in medieval culture [2001].pdf
MICROBIAL INTERACTION PPT/ MICROBIAL INTERACTION AND THEIR TYPES // PLANT MIC...
MICROBIAL INTERACTION PPT/ MICROBIAL INTERACTION AND THEIR TYPES // PLANT MIC...
Asms qc Will Thompson Duke
- 1. The GOAL… “That our differential expression data will be an accurate representation of the biological system measured, and that our colleagues who develop clinical diagnostics will find the data credible.”
- 2. The GOAL… my BELIEF… “That if I do not pay enough attention to experimental design and quality control, those colleagues will never believe me.” “That our differential expression data will be an accurate representation of the biological system measured, and that our colleagues who develop clinical diagnostics will find the data credible.”
- 3. Variability in Label-Free Proteomics Workflows Sample Prep Data Collection Minimize and Measure Variability!
- 4. Sample Prep: Procedure and Pitfalls Lysis Normalization Digestion SPE/Desalting Dry and Reconstitute Detergent/Chaotrope Physical Stress mL/mg volume ratios Bradford/BCA/A280 Assay Constant protein content Constant volume Substrate concentration Constant Enz/Substrate Ratio Fresh reagents Mixing/Temperature/Time Enzyme Quality? Online/offline Commercial/Homemade Avoid where possible Speedvac/Lyophilize Solubility? Avoid where possible
- 5. Sample Prep: Controlling for Variability Lysis Normalization Digestion SPE/Desalting Dry and Reconstitute Controlling for variability Constant mass/volume ratios Constant Volume and [Protein] Protein Standards (SIL or “surrogate”) Peptide Standards (SIL or “surrogate”)
- 6. How to Assess Variability of a Workflow Zhang, Fenyo, and Neubert. J. Proteome Res. 2009, 8(3): 1285-1292 Method 2 (Neubert et al) 𝑆2 𝑡𝑜𝑡𝑎𝑙 = 𝑆2 1 + 𝑆2 2 + 𝑆2 3 …+𝑆2 𝑛 Method 1 (‘old school’) Biological Technical (Preparation) Analytical . . . .
- 7. Limiting and Measuring Variability in LC-MS/MS Analysis (Exemplar with n=6 Samples) “Technical-Replicate Heavy” Incorrect (Underestimation) Correct “Moderate Technical Replication” (“90/10 approach”) “Singles + QC Pool” Analysis Order: 1. Randomization (if unknowns) 2. “Blocking” + Randomization (if known sample grouping)
- 8. Limiting and Measuring Variability in LC-MS/MS Analysis (Exemplar with n=6 Samples) “Singles + QC Pool” Technical Variance (%CV) Biological Variance (%CV) 0 5 10 15 20 25 30 35 2 3 4 5 6 7 8 9 10 Average%CV Number of Peptides Biological Variance (Avg) Technical Variance (Avg) 0 200 400 600 800 1000 5 15 25 35 45 55 65 75 85 95 PeptideCount % CV Biological Variance Technical Variance