DOI: 10.25338/b83h1z
title: MS/MS proteomics from: <em>Citrus sinensis</em> leaves in response to Diaphorina citri infestation and Huanglongbing disease

description: Huanglongbing (HLB) is a fatal citrus disease currently threatening all
 commercially relevant citrus varieties worldwide. In the United States,
 the putative causative agent, Candidatus Liberibacter asiaticus (CLas), is
 transmitted by the vector Diaphorina citri, commonly known as the Asian
 citrus psyllid (ACP). Progress towards understanding CLas and its role in
 HLB has been hindered by the inability to culture the bacterium and the
 inability to confidently detect it in diseased trees during the
 asymptomatic stage. To identify early changes in citrus metabolism in
 response to inoculation of CLas using its natural psyllid vector, leaves
 from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck)
 trees were exposed to CLas-positive ACP or CLas-negative ACP and
 longitudinally analyzed using transcriptomics (RNA sequencing), proteomics
 (liquid chromatography-tandem mass spectrometry), and metabolomics (proton
 nuclear magnetic resonance). At 4 weeks post-exposure (wpe) to psyllids,
 the initial HLB plant response was primarily to the ACP and, to a lesser
 extent, the presence or absence of CLas. Additionally, analysis of 4, 8,
 12, and 16 wpe identified 17 genes and one protein as consistently
 differentially expressed between leaves exposed to CLas-positive ACP
 versus CLas-negative ACP.. The results of this study inform identification
 of early detection molecular targets and contribute to the broader
 understanding of vector-transmitted plant pathogen
 interactions. There are two datasets related to this research MS/MS
 Proteomics: 10.25338/B83H1Z 1H NMR based
 metabolomics: 10.25338/B83P9Q
description: Whole <em>Citrus sinensis</em>
 leaves were collected throughout this longitudinal analysis. Citrus leaf
 proteins were extracted and precipitated, followed by peptide sample
 preparation, gel analysis, reduction/alkylation/trypsin digestion, C18
 column cleanup, and mass spectrometry data acquisition. Mass spectrometry
 was performed on a Fusion Exploris (Thermo Fisher Scientific) mass
 spectrometer with a Thermo Easy-nLC HPLC with autosampler. The resulting
 .raw files are provided in this submission.
description: # MS/MS Proteomics of Citrus sinensis Leaves ## Description of the data
 and file structure Protein extraction was carried out from whole leaf
 tissue collected from the following Tree IDs for the control, CLas(-) ACP
 exposed trees, and CLas(+) ACP exposed tree experimental groups: Control =
 1, 2, 11, 29 & 34; CLas(-) ACP: 8, 17, 23, 32 & 36; CLas(+) ACP =
 3, 10, 20, 33 & 35) at 0, 4, 8, 12, 16, 24, and 52 weeks post
 exposure. Samples underwent leaf protein extraction and precipitation,
 peptide sample preparation, gel analysis, reduction/alkylation/trypsin
 digestion, C18 column cleanup, and liquid chromatography mass spectrometry
 acquisition. Mass spectrometry was performed on a Fusion Exploris (Thermo
 Fisher Scientific) mass spectrometer with a Thermo Easy-nLC HPLC with
 autosampler. MS/MS Thermo `*.raw` files are stored in the folder
 OrangeTrees_ddaData.zip. Files were named using an internal laboratory
 naming scheme, but the provided *sample_information.csv* file describes
 which `.raw` file corresponds to each (1) tree sample ID, (2) weeks post
 the start of the study that the samples were collected, and (3) the
 experimental group. For ease of review, the contents of
 the *sample_information.csv* file are duplicated in Table 1.  MS/MS Thermo
 *.raw files were converted to Mascot Generic Format (*.mgf) using
 msConvertGUI (64 bit; ProteoWizard) before downstream analysis. Table 1.
 MS/MS Thermo `*.raw` files and corresponding metadata  | File\_name |
 Tree\_ID | Timepoint\_of\_Collection | Experimental\_Group | |
 :--------------------------------------------------- | :------- |
 :------------------------ | :------------------ | |
 D\_2020\_0623\_RJ\_38\_b1-12dda.raw | 32 | 16 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_68\_b1-25dda.raw | 17 | 12 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_230\_b3-22dda.raw | 34
 | 12 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_34\_b1-10dda.raw
 | 29 | 52 weeks post-exposure | No ACP | |
 D\_2020\_0623\_RJ\_207\_b3-12dda.raw | 33 | 52 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_225\_b3-20dda.raw | 23 | 0 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_142\_b2-19dda.raw | 2 |
 0 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_250\_b3-31dda.raw |
 10 | 12 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_156\_b2-25dda.raw | 33 | 0 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_25\_b1-6dda.raw | 32 | 52 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_210\_b3-13dda.raw | 1 |
 0 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_235\_b3-24dda.raw |
 34 | 8 weeks post-exposure | No ACP | |
 D\_2020\_0623\_RJ\_52\_b1-18dda.raw | 36 | 16 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_176\_b2-34dda.raw | 3 | 12 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_189\_b3-4dda.raw | 11 |
 52 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_158\_b2-26dda.raw |
 8 | 52 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_153\_b2-24dda.raw | 20 | 4 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_133\_b2-15dda.raw | 20 | 24 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_162\_b2-28dda.raw | 11
 | 4 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_203\_b3-10dda.raw
 | 8 | 16 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_131\_b2-14dda.raw | 35 | 0 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_192\_b3-5dda.raw | 17 | 24 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_86\_b1-33dda.raw | 8 |
 8 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_135\_b2-16dda.raw | 8 | 24 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_149\_b2-22dda.raw | 20 | 52 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_29\_b1-8dda.raw | 3 |
 52 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_88\_b1-34dda.raw | 2 | 12 weeks post-exposure | No ACP
 | | D\_2020\_0623\_RJ\_212\_b3-14dda.raw | 20 | 12 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_174\_b2-33dda.raw | 23 | 4 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_257\_b3-34dda.raw | 17
 | 4 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_178\_b2-35dda.raw | 32 | 8 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_246\_b3-29dda.raw | 11 | 8 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_185\_b3-2dda.raw | 23 | 52
 weeks post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_117\_b2-8dda.raw
 | 36 | 0 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_43\_b1-14dda.raw | 36 | 52 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_120\_b2-9dda.raw | 20 | 8 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_32\_b1-9dda.raw | 35 |
 16 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_261\_b3-36dda.raw | 1 | 12 weeks post-exposure | No ACP
 | | D\_2020\_0623\_RJ\_16\_b1-2dda.raw | 29 | 24 weeks post-exposure | No
 ACP | | D\_2020\_0623\_RJ\_187\_b3-3dda.raw | 17 | 0 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_147\_b2-21dda.raw | 10 | 16 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_169\_b2-31dda.raw | 32
 | 4 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_36\_b1-11dda.raw | 2 | 16 weeks post-exposure | No ACP
 | | D\_2020\_0623\_RJ\_83\_b1-32dda.raw | 29 | 4 weeks post-exposure | No
 ACP | | D\_2020\_0623\_RJ\_196\_b3-7dda.raw | 34 | 24 weeks post-exposure
 | No ACP | | D\_2020\_0623\_RJ\_252\_b3-32dda.raw | 33 | 4 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_129\_b2-13dda.raw | 8 |
 0 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_79\_b1-30dda.raw | 10 | 4 weeks post-exposure | CLas(+)
 ACP | | D\_2020\_0623\_RJ\_259\_b3-35dda.raw | 17 | 8 weeks post-exposure
 | CLas(-) ACP | | D\_2020\_0623\_RJ\_228\_b3-21dda.raw | 11 | 12 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_104\_b2-2dda.raw | 1 | 24
 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_255\_b3-33dda.raw | 1
 | 4 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_241\_b3-27dda.raw
 | 32 | 12 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_50\_b1-17dda.raw | 17 | 52 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_47\_b1-16dda.raw | 20 | 16 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_113\_b2-6dda.raw | 11 |
 0 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_124\_b2-11dda.raw |
 34 | 0 weeks post-exposure | No ACP | |
 D\_2020\_0623\_RJ\_115\_b2-7dda.raw | 3 | 16 weeks post-exposure | CLas(+)
 ACP | | D\_2020\_0623\_RJ\_77\_b1-29dda.raw | 1 | 8 weeks post-exposure |
 No ACP | | D\_2020\_0623\_RJ\_23\_b1-5dda.raw | 33 | 24 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_63\_b1-23dda.raw | 8 |
 4 weeks post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_20\_b1-4dda.raw
 | 10 | 52 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_219\_b3-17dda.raw | 3 | 0 weeks post-exposure | CLas(+)
 ACP | | D\_2020\_0623\_RJ\_27\_b1-7dda.raw | 17 | 16 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_106\_b2-3dda.raw | 32 | 24 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_140\_b2-18dda.raw | 34
 | 52 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_61\_b1-22dda.raw
 | 33 | 12 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_214\_b3-15dda.raw | 2 | 52 weeks post-exposure | No ACP
 | | D\_2020\_0623\_RJ\_81\_b1-31dda.raw | 8 | 12 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_248\_b3-30dda.raw | 2 | 4 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_56\_b1-20dda.raw | 10 | 0
 weeks post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_160\_b2-27dda.raw
 | 35 | 12 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_167\_b2-30dda.raw | 23 | 8 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_223\_b3-19dda.raw | 29 | 16 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_65\_b1-24dda.raw | 35 | 8
 weeks post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_165\_b2-29dda.raw
 | 33 | 8 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_232\_b3-23dda.raw | 29 | 12 weeks post-exposure | No
 ACP | | D\_2020\_0623\_RJ\_216\_b3-16dda.raw | 29 | 0 weeks post-exposure
 | No ACP | | D\_2020\_0623\_RJ\_221\_b3-18dda.raw | 23 | 16 weeks
 post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_237\_b3-25dda\_20200716231938.raw | 29 | 8 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_126\_b2-12dda.raw | 36 | 24
 weeks post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_70\_b1-26dda.raw
 | 3 | 8 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_111\_b2-5dda\_20200704161741.raw | 35 | 52 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_59\_b1-21dda.raw | 36 |
 8 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_194\_b3-6dda.raw | 10 | 24 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_201\_b3-9dda.raw | 23 | 24 weeks
 post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_205\_b3-11dda.raw | 2 |
 24 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_45\_b1-15dda.raw |
 1 | 52 weeks post-exposure | No ACP | |
 D\_2020\_0623\_RJ\_171\_b2-32dda.raw | 2 | 8 weeks post-exposure | No ACP
 | | D\_2020\_0623\_RJ\_74\_b1-28dda.raw | 36 | 12 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_198\_b3-8dda.raw | 11 | 16 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_54\_b1-19dda.raw | 32 | 0
 weeks post-exposure | CLas(-) ACP | | D\_2020\_0623\_RJ\_138\_b2-17dda.raw
 | 33 | 16 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_72\_b1-27dda.raw | 23 | 12 weeks post-exposure |
 CLas(-) ACP | | D\_2020\_0623\_RJ\_122\_b2-10dda.raw | 20 | 0 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_239\_b3-26dda.raw | 36
 | 4 weeks post-exposure | CLas(-) ACP | |
 D\_2020\_0623\_RJ\_180\_b2-36dda.raw | 35 | 4 weeks post-exposure |
 CLas(+) ACP | | D\_2020\_0623\_RJ\_151\_b2-23dda.raw | 3 | 24 weeks
 post-exposure | CLas(+) ACP | | D\_2020\_0623\_RJ\_243\_b3-28dda.raw | 34
 | 4 weeks post-exposure | No ACP | | D\_2020\_0623\_RJ\_92\_b1-36dda.raw |
 10 | 8 weeks post-exposure | CLas(+) ACP | |
 D\_2020\_0623\_RJ\_144\_b2-20dda.raw | 34 | 16 weeks post-exposure | No
 ACP | | D\_2020\_0623\_RJ\_18\_b1-3dda.raw | 1 | 16 weeks post-exposure |
 No ACP | | D\_2020\_0623\_RJ\_90\_b1-35dda.raw | 3 | 4 weeks post-exposure
 | CLas(+) ACP | | D\_2020\_0623\_RJ\_108\_b2-4dda.raw | 11 | 24 weeks
 post-exposure | No ACP | | D\_2020\_0623\_RJ\_41\_b1-13dda.raw | 35 | 24
 weeks post-exposure | CLas(+) ACP | 
 
 There are two datasets related to this research * MS/MS
 Proteomics: 10.25338/B83H1Z (this one) * 1H NMR based
 metabolomics: 10.25338/B83P9Q