D**A
发帖数: 311 | 1 最近把一个未知蛋白送去做mass spec sequencing. 结果让人不能理解，看有没有mass
spec达人能帮忙分析下。
蛋白是从细胞里提的，跑10% sds-page, coomassie blue stain，根据biorad的marker
来看，大小应该是45-48kd之间。
切下胶去做mass spec （nano-LC, MS/MS, ESI），结果显示为一个33kd的蛋白 （79个
peptide， 53%coverage）。当然还参杂了其他蛋白，但是peptide数量不多。
从33kd到45kd, 差了30%多。。。我们在想，有没有可能mass spec的人搞砸了。
希望有人可以帮忙分析下，先谢了。 |
|
y*****s
发帖数: 1047 | 2 This is not about the mass accuracy. MS only looks at the m/z of peptide
ions and fragment ions and match them with the theoretic values calculated
from known genome. If the observed and theoretic values match with each
other, then the peptide is identified. OP's question is really how can a
45kDa protein have a sequence of a 33kDa protein. |
|
s*********n
发帖数: 128 | 3 http://link.springer.com/article/10.1007/s13361-014-1059-9
Herein, we developed two novel cysteine-based quantitative proteomics
workflows. The first method is cysteine-selective precursor dimethyl
labeling (cysDML). In this workflow, cysteinyl-peptides are captured on a
commercially available Thiopropyl Sepharose 6B resin and captured peptides
are labeled on resin with either light (–C2H6) or heavy (–13C2 2H6)
dimethyl tags [43]. CysDML appears to be a convenient, efficient, accurate,
and affor... 阅读全帖 |
|
f*******K
发帖数: 34 | 4 我知道这篇文章，Sample Multiplexing with Cysteine-Selective Approaches:
cysDML and cPILOT, 相关工作在ASMS会议报道过。他们所用的方法基本还是基于传统
方法改良如Thiopropyl Sepharose 6B resin和Cys TMT，这些基于抗体和resin方法的
富集效率比较低，从鉴定数目就可以看到。我们的富集效率可以达到97%，很轻松鉴定
到10000+ unique peptides。
目前没有同时含有iodoacetamide+phosphate的tag。phosphate可能会被phosphatase酶
切掉，phosphonate不能，因此更加稳定。
至于为什么要富集Cys peptide,因为其low abundance,essential for the biological
activity and structure, highly sensitive and reactive.
同时富集目的是研究PTM crosstalk.在我的文章里面有很好的例子，protein tyrosine
... 阅读全帖 |
|
f*******K
发帖数: 34 | 5 Phosphopeptides是亲水性的，tag标记后的Cys peptides是相对疏水性的，可以通过
HILIC相对区分开，降低他们的相互影响。和以前的方法相比，鉴定数目明显胜出。
To dahuzi,我不知道你这个蛋白的相对丰度，不好给具体建议。不过如果你的蛋白质
里面那些包含你感兴趣的PTMs sites的peptides能够通过常规LCMSMS鉴定到,那么我的
方法应该也能。不过对单个蛋白质，你可以考虑做topdown,应该更直接。 |
|
g*****x
发帖数: 3283 | 6 peptide的de novo sequencing是非常非常old的东西了。。。。。但技术上来说，已经
有了DNA测序技术，再发展peptide测序就没太大意义了；反过来，放着那么大一个cDNA
database不用，不是傻么 |
|
c*********r
发帖数: 1312 | 7 谢谢给我耐心讲解。纯化的单个已知蛋白cover 80-9x％，很强大。NGS测序不管是针对
个别基因的targeted sequencing还是复杂体系里，根据不同的技术对于丰度足够高的
序列，coverage能达到90%以上。
所以我更关心的是你后边说的这个，在复杂的体系里，cell lysate样本，miss了多少
的问题。确实我之前的理解有误，还请耐心指点。MS的原理是不是如果一个peptide在
data base里没有很好的match，是不是就直接skip了做下一个？还是说还会测完但是把
raw data保存着，以后有了更好的data base来run一遍。
我记得我们的core可以导出一个searchable的数据类型，这样的话以后我们有了新的
annotation，新的序列添加进去，新的PTM，我们可以重新search我们的数据。是这样
的吗？
peptide |
|
G***G
发帖数: 16778 | 8 peptide的原数据和ngs的reads一样。
如果match不好，那么peptide得到的匹配分数就很低。但是你要是不介意也可以使用。
ngs也是reads和genome sequences搜索。为何匹配分值就高一些呢？ |
|
a********6
发帖数: 76 | 9 什么叫 “想分盐和PEPTIDE”？把盐和PEPTIDE分开？ |
|
s********m
发帖数: 748 | 10 请问用Qtrap得到的data做Mascot search的时候parameter如何设置？ 我按照公司给的
参数好像结果不是很好。我之所以说不好是因为同一个样品我用LTQ做的时候多发现了
很多peptide，大概十几倍，感觉不太正常。我LTQ的peptide tol is 800ppm, MS/MS
is 0.6Da， instrument type is ESI-trap, 请问这三项Qtrap一般该如何设置？还有
其他需要特别注意的吗？
如果这些都不是主要问题的话，我不知道是不是实验本身的问题了，希望哪位熟悉此仪
器的高手给点建议， 谢谢 |
|
x********e
发帖数: 1064 | 11 Incomplete Fmoc deprotection in solid-phase synthesis of peptides
BJARNE DUE LARSEN, ARNE HOLM
International Journal of Peptide and Protein Research
Volume 43, Issue 1 , Pages1 - 9
1994 Munksgaard
please sent to x**********[email protected]
Thanks. |
|
c******m
发帖数: 884 | 12 小分子(PK)和大分子(peptide, proteins)用的MS/MS主要区别是什么？
QTRAP (Linear Ion Trap + Quadrupole) 可以用来测 peptide 和 protein 吗？
感谢各位大牛，帮帮忙吧。 |
|
c*****t
发帖数: 198 | 13 【 以下文字转载自 Biology 讨论区 】
发信人: compact (support), 信区: Biology
标 题: ebook help
发信站: BBS 未名空间站 (Mon Feb 14 14:51:57 2011, 美东)
Self-Assembling Peptide Systems in Biology, Medicine and Engineering
http://www.amazon.com/Self-Assembling-Peptide-Systems-Medicine-
Engineering/dp/9048157404/ref=sr_1_1?s=books&ie=UTF8&qid=1297712199&sr=1-1
Thank you very much. |
|
b*********2
发帖数: 190 | 14 You may start the session with analyzing simple peptides, or peptide
mixtures. Then follow with the digested protein and database search.
3 hours is pretty short,especially if they have no hands-on experience with
MALDI before. |
|
b*********2
发帖数: 190 | 15 如果我是你，我会这么设计：
买三种peptide（比如angiotensin之类的），三种protein（比如myoglobin,beta-
lactoglobulin等常见的），实验之前你把protein给digest好，作为三个unknown。
前半节，准备matrix，让他们自己混各种peptide点板玩，对谱有个大致的印象。如果
有时间可以做MS/MS，倒推sequence。不过如果他们完全没有接触过，这里还需要一点
时间讲解b，y ion的基础知识。
后半节，把unknown protein digests发给他们，得到谱图，分别用手动计算和
database search来判断哪个是什么protein。
对于de novo sequencing，可以用protein prospector作为依据，MS/MS和digest都可
以计算。 |
|
f*********e
发帖数: 1144 | 16 请教一下：
我有俩peptide, Positive mode死活出不来，想试一下negative mode,500-3500 m/z
range
1. 用什么matrix阿？如果跟positive mode一样，要不要加什么东西help
deprotonated阿？
2. 有什么经验比如什么样AA组成的tryptic digested peptide不容易protonated,适合
negative mode呢?
多谢！ |
|
b*****y
发帖数: 175 | 17 Thanks again for all your new inputs!
Additional information:
1. I used Vydac MS C18 capillary column.
2. The sequence coverage of my protein (from trypsin digested peptides MS
analysis) is consistent (80%) for both non-treated and treated samples. So
my confusion is since the protein identity is confirmed from peptide MS
analysis, why it does not show in protein MS analysis.
3. We do not have MALDI in the lab so it is hard to check using another MS
technique.
4. I found out the 28498 Da peak in... 阅读全帖 |
|
k****o
发帖数: 728 | 18 我的条件是37 C，20 mM NaIO4, pH4。 用Na2SO3 quench reaction。 30min时候大概原始
glycopeptide和目标开环的peptide各50%，没有明显的副产物。 1h后，原始
glycopeptide和目标产物1:9，但两者峰面积都大大下降。不知道大量peptide跑哪里去
了。 |
|
|
n******e
发帖数: 1246 | 20 Silica-Precipitating Peptides Isolated from a Combinatorial Phage Display
Peptide Library
Authors: Rajesh R. Naik1; Lawrence L. Brott1; Stephen J. Clarson2; Morley O.
Stone1
Source: Journal of Nanoscience and Nanotechnology, Volume 2, Number 1,
February 2002 , pp. 95-100(6)
发c*******[email protected]
谢谢啦 |
|
y*****s
发帖数: 1047 | 21 广告都多得很
Posted/Revised: 5/2/2012
Company/Institute: Pfizer Inc
Department:
Position: 2 Year Postdoctoral Fellow – Protein Quantitation in Tissues
by Mass Spectr
Job Location: Andover, MA United States
Description: 2 year Postdoctoral Fellow – Protein Quantitation in
Tissues by Mass Spectrometry and Immunoanalytical Techniques A Postdoctoral
Fellowship is available in Pfizer’s Pharmacokinetics Dynamics and
Metabolism New Biological Entities (PDM-NBE) in Andover, MA. The PDM ... 阅读全帖 |
|
c********c
发帖数: 80 | 22 当时组里唯一一个亚洲人就是一个四年级的日本师兄，很典型的那种让你记不住的日文
音传写（不知道他的汉字名字）。我们接触的次数实在有限，我现在对他的印象就是长
头发，戴眼镜，然后就是他的抑郁与忧愁。我最后一次见到他，是在一天晚上，他在吃
饼干，心不在焉地翻着那本strategic application of named reactions的书。他和我
说，他已经决定quit phd回日本了。也许是见我当时面有惊恐之色，他接着说，Steve
还是一个不错的老板，我决定quit了，他也很尊重我的决定，还给我写了推荐信。。。
于是很快，他就消失了，我便继承了这个师兄的hood，bench，和desk。我曾经试图了
解到底发生了什么，结果发现，他在人们的记忆中消失的很快，正如他的名字在网页上
消失一样。我听说的是，他因为全组从B大学搬到了A大学，到了一个新地方不适应，所
以抑郁了。一个外国人，不远万里来到美国，因为在相距几个小时的两个美国城市间搬
了家，就抑郁了。。。
老板说，既然你对合成感兴趣，就接手这个project吧。这是一个挺小，挺简单的
macrocycle，做它其实是为了验证方法。老... 阅读全帖 |
|
x**********0
发帖数: 33 | 23 POSITION SUMMARY
A Senior Scientist who will play a key role in new drug characterization and
analysis using LC/MS in research and development. Major responsibilities
include bioanalytical assay development for drug DMPK studies and peptide/
protein and antibody analysis in support of drug candidate selection,
preclinical and IND-enabling studies
ESSENTIAL FUNCTIONS
- Peptide/protein and antibody analysis using Agilent QTOF
- Developing in vitro DMPK assays using SCIEX QTRAP including meta... 阅读全帖 |
|
x*o
发帖数: 1037 | 24 Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers
西北的Stupp
Science, November 2001, 294, 1684
他们所合成的PA有三点features:
一, 为了增强fiber的强度，在peptide-amphiphile(PA)中引进了四个cysteine aa.在氧
化态下cysteine的thiol在fiber的表面形成双硫键，从而增强fiber的强度
二, 在PA中引进phosphoserine residue, 使hydroxyapatite(HA)更容易在fiber上成核。
三, 在PA中引入Arg-Gly-Asp以提高表面对细胞的附着和生长。
感觉有两个interesting的地方：
1, 可以用pH值控制PA可逆地self-assemble形成fiber
2, 在self-assembly以后，进行mineralize, 得到的HA的c轴与fiber的长轴方向相同。此
性质与“is the same as that observed between collage |
|
m***n
发帖数: 266 | 25 Nature Biotechnology, Vol 21, 10, Oct 2003, 1171.
Shuguang Zhang
Fabrication of novel biomaterials through molecular self-assembly
我的看法:
1.natural or natural mimic peptide作为building block, instead of conventional
polymer, 看起来是很有前途的发展趋势. 对于Tissue engineering, cell patterning
and etc 尤其如此.
2.不知道有没有人做peptide combinatorial library,这种力气活好啊:-)
欢迎拍砖. |
|
h*******r
发帖数: 182 | 26 The logic that increase of HLA type leads to inability of MHC binding to
antigen peptide is not reasonable. What I believe is that this increase HLA
type is more like the peptide, therefore these people will not produce
antibody. This is called anergy. Otherwise autoimmune disease will ensue.
Opposite example is rheumatic fever post-streptococcus infection(Type II
hypersensitivity against heart, joint, brain tissue), or more accuarately
like PAIR that happened after Clamydia or Campy infection. |
|
z**********4
发帖数: 467 | 27 Pure assumption:
C-peptide level can only be released by normal "islet cells". Insulinoma
does not contain normal "islet cells" which could not efficiently cleave pro
-insulin peptide to Cpeptide. Waiting for more evidence. |
|
D*********t
发帖数: 140 | 28 I agree with hmis! First, the low limit of C peptide level together with a
high limit insulin level rules out insulinoma. This is because C peptide is
cleaved from proinsulin together with insulin and thus it should be always
parallel to the insulin level. Second, I think the possibility of pituitary
disease is the low level of cortisol. In hypoglycemia condition, cortisol
should be increased as response to stress. But cortisol in this patient is
still in low limit, indicating a failure to respo... 阅读全帖 |
|
h*******y
发帖数: 1220 | 29 Sorry for hacking your thread. Those who have not taken CK may learn a point
or two:
From wiki
VIPoma：A VIPoma (also known as Verner Morrison syndrome, after the
physicians who first described it)[1] is a rare (1 per 10,000,000 per year)
endocrine tumor,[2] usually (about 90%) originating from non-β islet cell
of the pancreas, that produce vasoactive intestinal peptide (VIP). It may be
associated with multiple endocrine neoplasia type 1.
The massive amounts of VIP in turn cause profound and chro... 阅读全帖 |
|
z***q
发帖数: 175 | 30 今天去考试中心模拟考试，遇到这样一道题。虽然选对了（答案是c）但是没有clue。
觉得就是insulinoma，但不明白为什么insulin正常高值，c－peptide也不高。
大家来看看：
48. A previously healthy 32-year-old woman who
works as a nurse comes to the emergency
department because of a 3-week history of
episodes of dizziness, nausea, and profuse
sweating that resolve with eating. She does not
smoke. She drinks four glasses of wine weekly.
Vital signs are within normal limits. Physical
examination shows no abnormalities. While in
the emergency department, she becomes dizzy
a... 阅读全帖 |
|
e*******a
发帖数: 246 | 31 normally c-peptide is elevated in insulinoma. But there are non-typical
insulinoma patients whose c-peptide level is relatively low; Please refer
to this case report: http://www.ncbi.nlm.nih.gov/pubmed/17146148 |
|
V*I
发帖数: 46 | 32 【 以下文字转载自 Biology 讨论区 】
发信人: VII (I,II,III,IV,V,VI,?,VIII), 信区: Biology
标 题: 求文章两篇，发包子
发信站: BBS 未名空间站 (Tue Oct 9 10:17:05 2007), 转信
1
Protein and peptide parental controlled delivery
Author(s): Pawar R, Ben-Ari A, Domb AJ
Source: EXPERT OPINION ON BIOLOGICAL THERAPY 4 (8): 1203-1212 AUG 2004
Document Type: Review
Language: English
2
Title: Controlled delivery of peptides and proteins
Author(s): Degim IT (Degim, I. Tuncer), Celebi N (Celebi, Nevin)
Source: CURRENT PHARMACEUTICAL DESIGN 13 (1) |
|
h*****t
发帖数: 1226 | 33 I do not agree with your definition.
Proteomics, at beginning probably is derivated from protein characterization
,
but it has quite different focus and aspects.
Nowadays, proteomics is not just using mass spec to detect protein/peptides,
a
lot of other techniques have been applied into this area, most importantly
is
Statistics/ Computational biology. And now proteomics is far beyond using
mass spec to detect protein/peptides, like structural proteomics,
interaction
proteomics, subcellular pr |
|
c******m
发帖数: 884 | 34 小分子(PK)和大分子(peptide, proteins)用的MS/MS主要区别是什么？
QTRAP (Linear Ion Trap + Quadrupole) 可以用来测 peptide 和 protein 吗？
感谢各位大牛，帮帮忙吧。 |
|
m*1
发帖数: 41 | 35 有分离peptide and polypeptide的经验 small peptide MW小于500的 polypeptide MW
大于3500的都有 这个算不算大分子经验？ |
|
x**********7
发帖数: 973 | 36 我以前是做蛋白结晶的，后来博后做了很久的structure-based drug discovery 和
inhibitor 抑制机理研究。 同时本人以前有化工经验
一年前终于脱离学校苦海，找到一个小公司做ProcessDevelopment，基本就是服务于
peptide manufacturing, 主要研究纯化，杂质，过程优化 等等
最近又开始做peptide drug 的formulation 工作，并且机缘巧合，在做两个generic
drug formulation development ，同时现在要负责设计，建设一个生产facility，并
且负责license 生产工艺，PD， 放大，生产
现在的工作比以前学校的，我觉着有意思的多，有意义的多
唯一心中还是不太明确的是，这个方向走下去前途如何 （我岁数较大，首先担心的当
然是job security），我们这里是偏僻的南方，周围没有类似工作，不知道如果工作出
了意外，再找容易与否 （个人不太会去加州，这行当在那里挣得工资活不下去）
现在药厂整天裁员，不知道PD这块招人的情况如何？ 过两年在东部一个像我这样的人
如果找工... 阅读全帖 |
|
x**********0
发帖数: 33 | 37 POSITION SUMMARY
A Senior Scientist who will play a key role in new drug characterization and
analysis using LC/MS in research and development. Major responsibilities
include bioanalytical assay development for drug DMPK studies and peptide/
protein and antibody analysis in support of drug candidate selection,
preclinical and IND-enabling studies
ESSENTIAL FUNCTIONS
- Peptide/protein and antibody analysis using Agilent QTOF
- Developing in vitro DMPK assays using SCIEX QTRAP including meta... 阅读全帖 |
|
|
f****n
发帖数: 723 | 39 Information theory in prediction of cleavage sites of signal peptides.
Protein and Peptide Letters, 12, 339-342
这鬼杂志竟然要$70一篇文章! |
|
j****e
发帖数: 245 | 40 Sleep is one of the many topics in psychology. Unfortunately, I don't know
much detail about its biological mechanism.
Below are some of the sleep substances currently receiving most attention:
delta-sleep-inducing-peptide (DSIP), muramyl peptides, interleukin-1,
sleep-promoting substance (SPS) and prostaglandin D2.
For further more detailed information, you can refer to the book below:
Endogenous Sleep Substances and Sleep Regulation
Proceedings of the Taniguchi Symposia on Brain Sciences Volu |
|
y****e
发帖数: 71 | 41
You are misunstanding here. We are talking about knowing peptide sequence,
reverse engeneering DNA sequence which can make this peptide in vivo.
Chemical synthesis protein is a hell of work. |
|
y****e
发帖数: 71 | 42
//faint
Short Peptide Chain, Long peptide chain
DNA的高级结构也许不是那么可变，其中涉及Scarfold protein, 和matrix。我
觉得还是有规律可以找的。
一直有一种印象（可能是错误的）。chaperone似乎是稳定folding中间态，防止
non-specific hydrophobic interaction导致的蛋白聚合和沉淀。不知道在search
正确folding structure时到底有多少催化作用。希望有人指点一二。 |
|
l****l
发帖数: 246 | 43 microarray不只是DNA array，还有peptide array，peptide array起步没多久，很多
人都在搞 |
|
f**d
发帖数: 768 | 44 这是一本计算神经科学的优秀著作，全文拷贝这里（图和公式缺），有兴趣的同学可以
阅读
如需要，我可以分享PDF文件（－－仅供个人学习，无商业用途）
From Computer to Brain
William W. Lytton
From Computer to Brain
Foundations of Computational Neuroscience
Springer
William W. Lytton, M.D.
Associate Professor, State University of New York, Downstato, Brooklyn, NY
Visiting Associate Professor, University of Wisconsin, Madison
Visiting Associate Professor, Polytechnic University, Brooklyn, NY
Staff Neurologist., Kings County Hospital, Brooklyn, NY
In From Computer to Brain: ... 阅读全帖 |
|
w*******y
发帖数: 60932 | 45 quote
Description: ELITE Gourmet is the perfect blend of Ion-Exchange Whey Protein
Concentrates, Whey Protein Isolates, and Whey Peptides, combined with Milk
Protein rich in natural micellar caseines & caseinates plus added calcium
caseinates. By combining these extraordinary and top quality protein sources
Elite Gourmet satisfies your tastebuds & your protein diet needs in one
delicious shake.
ELITE GOURMET PROTEIN contains high levels of Glutamine and Glutamine
Peptides as well as substantial |
|
d***a
发帖数: 13752 | 46 Fu并不在Department of Pharmacology吧。
看下面这个publication，1997年时，Fu所在的系叫Departments of Pathology,
Surgery, Physiology, and Medicine。这个系现在已经找不到了，应该是重组了。
这也可以解释Fu的简历中，毕业专业的变化。
http://www.pnas.org/content/94/10/5296.short
Amyloid-β peptide–Receptor for Advanced Glycation Endproduct interaction
elicits neuronal expression of macrophage-colony stimulating factor: A
proinflammatory pathway in Alzheimer disease
Shi Du Yan*,
Huaijie Zhu*,
Jin Fu*,
Shi Fang Yan*,
Alex Roher†,
... 阅读全帖 |
|
s********n
发帖数: 26222 | 47 方舟子在此文中说“虫子不吃的， 人能吃吗”是中国人的质疑， 而美国人是不会问这
样的问题的， 这显然是骗人的。见下文和其中引用的文献， 其中不少是美国人的科研
。
"Comments on the human health impact of Bacillus thuringiensis toxin gene
product in genetically modified crops"
EPA Review Docket Number OPP-00678B
Professor Joe Cummins
Professor Emeritus of Genetics
University of Western Ontario
I have studied the Environment Protection Agency (EPA) document "Bt Plant-
Pesticides Biopesticides Registration Action Document B. HUMAN HEALTH
ASSESSMENT" and comment in the following ... 阅读全帖 |
|
l********k
发帖数: 14844 | 48 blue cross/blue shield的classic PPO保险，包每年免费体检一次。去了，抽血，血常规、
生化14项、血脂、维生素D等等一共10项内容。过了几天收到账单，保险公司一分钱没掏，全算到
deductable里，没算成preventative care.
打电话过去咆哮数次，到目前为止给的理由是，奥巴马有个医改，依照这个改革，常规体检验血的内
容有很大变化。你账单上列的项目不在巴马医改后的验血常规项目中。
问对方，你们年检包括验血么？如果项目正确，billing code正确，你们给不给包100%?
对方说，是。
又问对方，如果一个bill里的部分项目在报销清单中，部分不在，你们会不会分开计算。
对方回答是，会分开计算。
我的单子10项，全部都不在他这个“清单”中。
继续问对方：巴马这个改革法案的名字是什么？
对方去查，放了5分钟音乐，回来说：不知道。
我给对方提示：是不是patient protection and affordable care act of 2010
(PPACA)
对方说：可能吧。
对话当中对方及其狡诈和不耐烦，多次想把话题重点引导我没有达到... 阅读全帖 |
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j*****p
发帖数: 24000 | 49 内源性胰岛素有C peptide
外源性没有这个
一查就知道了 |
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k****z
发帖数: 1863 | 50 一群眼红的中国人傻逼：
http://www.pnas.org/content/94/10/5296.short
Amyloid-β peptide–Receptor for Advanced Glycation Endproduct interaction
elicits neuronal expression of macrophage-colony stimulating factor: A
proinflammatory pathway in Alzheimer disease
Shi Du Yan*,
Huaijie Zhu*,
Jin Fu*,
Shi Fang Yan*,
Alex Roher†,
Wallace W. Tourtellotte‡,
Tripathi Rajavashisth§,
Xi Chen*,
Gabriel C. Godman*,
David Stern*, and
Ann Marie Schmidt*
- Author Affiliations
*Departments of Pathology, Surger... 阅读全帖 |
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