1）The first two lysine acetylomes of Arabidopsis leaves were reported in 2011, with only around 100 lysine acetylation sites identified (Finkemeier et al, 2011; Wu et al, 2011).
with only around 100 lysine acetylation sites identified.
with +noun+Ved复合结构。
eg：The thief was brought in with his hands tied.
2）Tremendous advances in mass spectrometry, improvements in antibody reagents, and the optimization of the overall protocol now allows a more in-depth profiling of the Arabidopsis lysine acetylome.
n+n+n +v+宾语
Watching TV and reading books are really interesting！
3）To be able to quantify acetylome changes upon KDAC inhibitor treatment, we applied an isotopic dimethyl-labeling approach to differentially label two different protein samples (e.g., treatment and control), combined with an enrichment strategy for lysine-acetylated peptides (Fig 1A).
combined with an enrichment strategy for lysine-acetylated peptides :分词作状语。
To be able to quantify acetylome changes upon KDAC inhibitor treatment,目的状语。
4）For this procedure, proteins extracted from leaves were processed and
trypsin-digested via filter-assisted sample preparation.
表示目的连词
For this procedure
For this reason, prices can supposedly never go down.
For this reason，our stock, which we think will last several months, are now completely sold out.
- Peptides were isotopically dimethyl-labeled, and samples for comparison were pooled.
通常and表示两个并列成分，并且相关，一般都不加逗号的，但如果前后不相关，或为了补充上文忘记提到的东西要加逗号的。
e.g.
- I deal with clients and organize meetings and events.
I went there and ate a apple。 - You could only really tell the effects of the disease in the long term, and five
years wasn't long enough.
-
For proteome quantifications, samples were collected at this step and the rest of the sample was further processed by hydrophilic interaction liquid chromatography fractionation to reduce the peptide complexity.
and 这里是并列且上下文联系。
For xxx， 目的 -
Six to seven fractions were collected and used for immuno-affinity enrichment using anti-acetyllysine agarose beads.
and 连接同一个主语。无逗号 -
Peptides were further processed for high-resolution mass spectrometry, and MaxQuant was used for the data analysis.
, and前后连接两个句子，不同主语。
9）Altogether the datasets presented here comprise 2,152 lysine acetylation sites (localization probability > 0.75) on 1,022 protein groups (6,672 identified protein groups in total, Table 1, Datasets EV1–EV5)—this corresponds to 959 novel acetylated proteins and 2,057 novel acetylation sites when compared to the previously published datasets for Arabidopsis.
—解释说明。
A MapMan functional annotation analysis (Thimm et al, 2004) was used for the classification of the lysine-acetylated proteins, applying the TAIR mapping and selecting all identified proteins of the proteome analysis as background population.
-
From the different cellular processes, the functional categories photosynthesis, tetrapyrrole synthesis, gluconeogenesis, redox, TCA cycle, as well as DNA and RNA regulation of transcription were identified as overrepresented as determined by a Fisher’s exact test, while processes such as hormone metabolism, cell wall, and secondary metabolism were underrepresented.
介词短语做状元, From the different cellular processes，
11）Additionally, we analyzed the local sequence context around the acetylation sites using iceLogo in combination with the Arabidopsis TAIR10 database with all identified proteins as background reference. -
Overall, negatively charged amino acids, such as glutamate and aspartate, were significantly enriched in the ?1, ?2, ?3 as well as +1 positions surrounding the lysine acetylation site.
-
The sequence motif surrounding the lysine acetylation site appeared different depending on the subcellular localization of the respective proteins.
-
For example, the negatively charged amino acids were more prominent on cytosolic and plastidial proteins in comparison with nuclear proteins, as well as the presence of a phenylalanine at position -2.
-
Interestingly, on the nuclear sequence motifs only positively charged amino acids were found at position +1 as well as generally more neutral amino acids such as glycine and alanine at positions -1 to -3, which are dominating on histone sequence motifs
状语前置：on the nuclear sequence motifs ，
正常：Only positively charged amino acids were found at position +1 as well as generally more neutral amino acids such as glycine and alanine at positions -1 to -3, which are dominating on histone sequence motifs， on the nuclear sequence motifs
image.png
as well as generally more neutral amino acids such as glycine and alanine at positions -1 to -3,
as well as 引导的同级比较，第一给as 是副词，第二个as引导词引导状语从句，其中从句的谓语必须省略。
如 He cooks as wel as her mother (does).
He speaks english as well as she (does)
本句应该是as well as generally more neutral amino acids such as glycine and alanine （were found）at positions -1 to -3.
15）Since 43% of all identified lysine-acetylated proteins are putative plastid proteins, we further analyzed the distribution of those proteins and number of acetylation sites in photosynthesis
since 引导的原因状语从句
Since 43% of all identified lysine-acetylated proteins are putative plastid proteins,
since引导的原因状语从句一般放于主句之前表示已知的、显然的理由通常被翻译成“既然”=now that，较为正式，但是语气比because弱。
例如：
Since you don't trust him,you should not employ him.
Considering （that） you donot trust hime， you should not hire him。
这里本句也该看改为：
Considering （that） 43% of all identified lysine-acetylated proteins are putative plastid proteins,
这里since 也可以改为now that 或者 In that
16） Proteins from the light harvesting complexes (LHC) of both PSII and PSI
were heavily acetylated with 29 lysine acetylation sites on LHCII and 16 on LHCI proteins.
主要：proteins
表语：were heavily acetylated
伴随状语：with 29 lysine acetylation sites on LHCII and 16 on LHCI proteins
定语： from the light harvesting complexes (LHC) of both PSII and PSI
17） All enzyme complexes involved in the carbon fixing reactions (Calvin–Benson cycle) as well as RuBisCO activase (RCA) contained four or more lysine acetylation sites
主语：All enzyme complexes ，as wel as RuBisCO activase (RCA)
定语：（that were）involved in the carbon fixing reactions (Calvin–Benson cycle)
谓语：contained
宾语：four or more lysine acetylation sites
18） Here, we selected two commonly used KDAC inhibitors, apicidin and tricho-
statin A (TSA), to target the RPD3/HDA1-type family of KDACs and
to profile their potential protein substrates.
主语：we
谓语：selected
宾语： two commonly used KDAC inhibitors,
同位语：apicidin and trichostatin A (TSA)
and 连接的目的状语：to target the RPD3/HDA1-type family of KDACs and
to profile their potential protein substrates.
状语：Here,
19） While apicidin was shown to specifically inhibit class I KDACs, TSA was described as a general inhibitor of class I and class II KDACs in HeLa cells
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