Tag: single cell proteomics

Note: The analyses were originated from citexs.com and I made several adjustments on the layout and content. For academic use only.

1.摘要
本文基于PubMed文献数据库，使用citexs赛特新思数据分析平台，对2012-01至2022-12关于 single cell 和 proteomics 研究进行文献分析及大数据挖掘，梳理该领域的发展历程，分析研究主题的热点变化等，将分析结果可视化，旨在对single cell 和 proteomics相关领域研究进行系统综述和趋势展望，探讨当前的研究动态及热点，挖掘分析尚需改进的内容，以期为后续研究提供参考。

2.数据来源
（1）数据来源于PubMed数据库
（2）时间跨度：2012-01至2022-12
（3）文献类型：article
（4）语种：English
（5）共检索到 1443 篇文献
（6）检索词：(single cell) AND (proteomics)

3.研究方法
本文采用文献计量学方法，以PubMed文献数据库为基础，使用citexs赛特新思数据分析平台，进行文献大数据挖掘，分别选择国家、机构、作者、关键词、期刊、关联疾病、关联基因等对象进行数据挖掘和分析，可视化呈现该领域的总趋势、分布情况、热点变化等。

4.1 年度发文趋势分析
以single cell 和 proteomics为关键词搜索，2012-01至2022-12的文献有 1443 篇，文献年均发文量132篇。如图1所示，2021达到年发文量顶峰310篇，2020增长率最快为42.33%，提示该领域的研究得到快速发展，处于快速上升阶段。

图1. 2012-01至2022-12 single cell 和 proteomics相关文献的年度发文趋势

4.2 研究国家分析
2012-01至2022-12，全球在 single cell 和 proteomics研究领域发文量前64的国家如图2所示， 在该领域发文量最多的国家是United States of America（606篇，42%），China（181篇，12.54%）和Germany（180篇，12.47%）位居第二和第三。

图2. 2012-01至2022-12 single cell 和 proteomics的研究国家分析

4.3 研究机构分析
2012-01至2022-12，全球在 single cell 和 proteomics 研究领域发文量前20的国家研究机构如图3所示，其中university of california和university of cambridge发文量占据前两名，分别发表了48篇和21篇，university of copenhagen发表了21篇，位于第三名。

图3. 2012-01至2022-12 single cell 和 proteomics的研究机构分析

4.4 研究作者分析
2012-01至2022-12，全球在 single cell 和 proteomics 研究领域发文量前30的作者见表1。该领域产出文献最多的作者是Richard D Smith，迄今为止一共发表21篇文献；Ying Zhu位居第二，发表了19篇文献；Ronald J Moore位居第三，已有14篇文献发表。 (声明：文献原始数据来源于pubmed，由于其部分机构缺失和部分杂志未收录，造成文章数量偏少，排名仅供参考！)

Rank	Author	Institute&country	No.
1	Richard D Smith	united states	21
2	Ying Zhu	united states	19
3	Ronald J Moore	united states	14
4	Wei-jun Qian	united states	13
5	Rui Zhao	united states	12
6	Tao Liu	united states	12
7	Nikolai Slavov	northeastern university, united states	11
8	Cecilia Lindskog	uppsala university, sweden	10
9	William B Chrisler	united states	9
10	Chia-feng Tsai	united states	8
11	Jing Zhou	united states	7
12	Ryan T Kelly	united states	7
13	Tujin Shi	united states	7
14	Angus I Lamond	university of dundee, united kingdom	6
15	Anil K Shukla	united states	5
16	Masanori Aikawa	brigham and women’s hospital, united states	5
17	Ryan T Kelly	brigham young university, united states	5
18	Fabian J Theis	institute of computational biology, germany	4
19	Jesper V Olsen	university of copenhagen, denmark	4
20	Ling Zhong	university of new south wales, australia	4
21	Mark J Raftery	university of new south wales, australia	4
22	Matthias Mann	max planck institute of biochemistry, germany	4
23	Paul D Piehowski	united states	4
24	Romain Huguet	united states	4
25	Rong Fan	yale university, united states	4
26	Sean Mackay	united states	4
27	Alexander Schmidt	university of basel, switzerland	3
28	Daniel Lopez-ferrer	united states	3
29	Fredrik Pontén	uppsala university, sweden	3
30	Joshua N Adkins	united states	3

4.5 发文期刊分析
2012-01至2022-12，以single cell 和 proteomics为关键词搜索，检索出论文1443篇，发文量排名前30的期刊见图4，其中刊载文献量最多的期刊是J Proteome Res（84篇）；Mol Cell Proteomics位居第二，刊载文献量60篇；Methods Mol Biol位居第三，刊载文献量54篇。

图4. 2012-01至2022-12 single cell 和 proteomics的发文期刊分析

4.6 关键词热点词频分析
论文关键词是对研究目的、研究对象、研究方法进行高度凝练与概括。基于关键词的分析能够反映某一研究领域某一时间段内主题演变趋势和研究热点。把single cell 和 proteomics作为为关键词搜索，时间跨度为2012-01至2022-12，如图5所示，出现频次前5的关键词分别是： proteomics，mass spectrometry，transcriptomics，metabolomics，single-cell proteomics.

图5. 2012-01至2022-12 single cell 和 proteomics的热点词频分析

4.7 关键词热度随时间变化分析
将2012-01至2022-12分为4个时间段，如图6表示与single cell 和 proteomics相关联的关键词词频在各个时间段的热度排名及排名变化情况。

图6. 2012-01至2022-12 single cell 和 proteomics不同时间段的热度排名及排名变化分析

4.8 关联基因分析
2012-01至2022-12，以single cell 和 proteomics为关键词搜索，检索出论文1443篇，如图7所示，其中文献量最多的TP53（95篇）；EGFR位居第二，文献量为71篇；AKT1位居第三，文献量66篇。

图7. 2012-01至2022-12 single cell 和 proteomics关联基因分析

5.1 AI推荐文献
根据搜索关键词single cell 和 proteomics，综合文献被引用数、发表时间、年份、影响因子等条件，推荐出30篇文献，见表2。

	Title	Journal	IF	PMID
1	Single-cell proteomics	Nat Methods	28.547	30573843
2	A dream of single-cell proteomics	Nat Methods	28.547	31406385
3	Defining the carrier proteome limit for single-cell proteomics	Nat Methods	28.547	33288958
4	Single-Cell Proteomics	Trends Biochem Sci		33653632
5	In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment	ACS Nano	15.881	34225455
6	Scaling Up Single-Cell Proteomics	Mol Cell Proteomics		34808355
7	Multiplexed single-cell proteomics using SCoPE2	Nat Protoc		34716448
8	Single-cell proteomics takes centre stage	Nature		34545225
9	Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell	Chem Sci	9.825	34163866
10	Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate	Cell Stem Cell	24.633	30880026
11	Single-Cell Proteomics for Cancer Immunotherapy	Adv Cancer Res	6.242	29941105
12	Single-cell Proteomics: Progress and Prospects	Mol Cell Proteomics		32847821
13	Driving Single Cell Proteomics Forward with Innovation	J Proteome Res		34597050
14	Single-cell proteomics reveals changes in expression during hair-cell development	Elife	8.140	31682227
15	Transformative Opportunities for Single-Cell Proteomics	J Proteome Res	4.466	29945450
16	Single-cell proteomics: A treasure trove in neurobiology	Biochim Biophys Acta Proteins Proteom		33845200
17	Mass Spectrometry-Based Analytical Strategy for Single-Cell Proteomics	Methods Mol Biol		34905166
18	Features of Peptide Fragmentation Spectra in Single-Cell Proteomics	J Proteome Res		34920664
19	Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics	Anal Chem		34967612
20	Spatial proteomics: a powerful discovery tool for cell biology	Nat Rev Mol Cell Biol	94.444	30659282
21	Single-cell transcriptomics combined with interstitial fluid proteomics defines cell type-specific immune regulation in atopic dermatitis	J Allergy Clin Immunol	10.793	32344053
22	Microfluidic Single-Cell Proteomics Assay Chip: Lung Cancer Cell Line Case Study	Micromachines (Basel)		34683198
23	Advancing single-cell proteomics and metabolomics with microfluidic technologies	Analyst	4.616	30351310
24	Replication of single-cell proteomics data reveals important computational challenges	Expert Rev Proteomics		34602016
25	Single Cell Proteomics Using Multiplexed Isobaric Labeling for Mass Spectrometric Analysis	Methods Mol Biol		34766268
26	In-Depth Mass Spectrometry-Based Single-Cell and Nanoscale Proteomics	Methods Mol Biol		33165848
27	A deeper look at carrier proteome effects for single-cell proteomics	Commun Biol		35194133
28	Imaging the future: the emerging era of single-cell spatial proteomics	FEBS J		33351222
29	An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics	Nat Commun	14.919	30814501
30	Microchip-based single-cell functional proteomics for biomedical applications	Lab Chip	6.799	28280819

5.2 经典文献
基于AI推荐文献共引用关系筛选出经典文献30篇，见表3。

	Title	Journal	IF	PMID
1	Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents	Mol Cell Proteomics	5.911	15385600
2	Cytoscape: a software environment for integrated models of biomolecular interaction networks	Genome Res	9.043	14597658
3	Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources	Nat Protoc		19131956
4	Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips	Nat Protoc	13.491	17703201
5	Large-scale analysis of the yeast proteome by multidimensional protein identification technology	Nat Biotechnol	54.908	11231557
6	Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS	Anal Chem	6.986	12713048
7	Global quantification of mammalian gene expression control	Nature		21593866
8	Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells	Proc Natl Acad Sci U S A		22203961
9	The Perseus computational platform for comprehensive analysis of (prote)omics data	Nat Methods	28.547	27348712
10	MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification	Nat Biotechnol	54.908	19029910
11	Mass spectrometry-based proteomics	Nature	49.962	12634793
12	Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells	Nat Commun	14.919	29491378
13	Ultrasensitive proteome analysis using paramagnetic bead technology	Mol Syst Biol	11.429	25358341
14	Proteomics. Tissue-based map of the human proteome	Science	47.728	25613900
15	Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets	Cell	41.582	26000488
16	Andromeda: a peptide search engine integrated into the MaxQuant environment	J Proteome Res	4.466	21254760
17	Skyline: an open source document editor for creating and analyzing targeted proteomics experiments	Bioinformatics		20147306
18	Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry	Nat Methods		24584193
19	Universal sample preparation method for proteome analysis	Nat Methods		19377485
20	Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo	Angew Chem Int Ed Engl	15.336	26756663
21	Mass Cytometry: Single Cells, Many Features	Cell		27153492
22	SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation	Genome Biol	13.583	30343672
23	Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum	Science		21551058
24	Quantitative analysis of complex protein mixtures using isotope-coded affinity tags	Nat Biotechnol	54.908	10504701
25	Single-cell western blotting	Nat Methods		24880876
26	The PRIDE database and related tools and resources in 2019: improving support for quantification data	Nucleic Acids Res	16.971	30395289
27	The MaxQuant computational platform for mass spectrometry-based shotgun proteomics	Nat Protoc	13.491	27809316
28	Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics	Mol Cell Proteomics	5.911	12118079
29	An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database	J Am Soc Mass Spectrom		24226387
30	Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ	Mol Cell Proteomics		24942700