Proteome of Penicillium funiculosum NCIM1228 and ∆Snf1 grown in glucose and Avicel in the presence as well as the absence of calcium
Data files
Feb 01, 2024 version files 20.47 GB
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Raw_data_MS.xlsx
32.91 MB
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README.md
8.76 KB
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Sample1.raw
2.06 GB
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Sample10.raw
1.67 GB
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Sample11.raw
1.69 GB
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Sample12.raw
1.69 GB
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Sample2.raw
1.76 GB
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Sample3.raw
1.53 GB
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Sample4.raw
1.56 GB
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Sample5.raw
1.62 GB
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Sample6.raw
1.68 GB
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Sample7.raw
1.72 GB
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Sample8.raw
1.73 GB
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Sample9.raw
1.71 GB
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workflow_with_q_value.txt
78.04 KB
Abstract
Penicillium funiculosum NCIM1228 and ∆Ampk were compared across calcium-limited and calcium-replete cellulosic conditions to assess changes within the proteome using quantitative mass spectrometry. These comparative proteomic data provide insights into cellular responses to produce and secrete cellulase during nutrient limitation, and the role of AMPK in cellulase secretion.
README: Title of Dataset: Proteome of Penicillium funiculosum NCIM1228 and ∆Snf1 grown in glucose and Avicel in the presence as well as the absence of Calcium.
Give a brief summary of dataset contents, contextualized in experimental procedures and results.
Sample1: NCIM1228 grown in Avicel, Sample 1
Sample2: NCIM1228 grown in Avicel, Sample 2
Sample3: NCIM1228 grown in Avicel, Sample 2
Sample4: NCIM1228 grown in Avicel with Calcium, Sample 1
Sample5: NCIM1228 grown in Avicel with Calcium, Sample 2
Sample6: NCIM1228 grown in Avicel with Calcium, Sample 3
Sample7: ∆Snf1 grown in Avicel, Sample 1
Sample8: ∆Snf1 grown in Avicel, Sample 2
Sample9: ∆Snf1 grown in Avicel, Sample 3
Sample10: ∆Snf1 grown in Avicel with calcium, Sample 1
Sample11: ∆Snf1 grown in Avicel with calcium, Sample 2
Sample12: ∆Snf1 grown in Avicel with calcium, Sample 3
Description of the data and file structure
Fle Name:
- Work flow with q-value.txt: includes the Work flow and steps used to process the samples and generate the .RAW data files
File Names of Raw data files generated by ThermoFisher Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer.
Sample1.raw
Sample2.raw
Sample3.raw
Sample4.raw
Sample5.raw
Sample6.raw
Sample7.raw
Sample8.raw
Sample9.raw
Sample10.raw
Sample11.raw
Sample12.raw
File Name: Raw_data_MS.xlsx; the file is the output file after data processing with proteome discoverer software.
The grey columns to the extreme left corresponds to three hierarchies in the rows. The dark gray column 1 corresponds to the proteins identified in the data set which are visible in the sheet by default, the dark gray column 2 is for opening the hidden rows which have the details of the peptides corresponding to a particular protein in the column 1, coloumn 3 will reveal the hidden rows having details of each peptide detected. The dark blue headers correspond to the light blue rows, the dark orange to the light orange/peach rows, and the dark gray headers correspond to the light gray rows.
The blue rows represents the proteins identified in the data sets. The headers for the blue rows are:
Column A : Protein FDR Confidence: Combined
Column B : Accession: Protein-ID of the expressed transcript
Column C : Description of protein function
Column D : Sequence of the Protein
Column E : Exp. q-value: Combined
Column F : Contaminant
Column G : Sum PEP Score
Column H : Coverage [%]
Column I : # Peptides detected
Column J : # PSMs
Column K : # Unique Peptides
Column L : # AAs : Total amino-acids in the protein
Column M : MW [kDa] : Size of the protein
Column N : calc. pI of the protein
Column O : Score Sequest HT: Sequest HT
Column P : # Peptides (by Search Engine): Sequest HT
Column Q : # Razor Peptides
Column R : Abundance: F1: NCIM1228 grown in Avicel, Sample 1
Column S : Abundance: F2: NCIM1228 grown in Avicel, Sample 2
Column T : Abundance: F3: NCIM1228 grown in Avicel, Sample 3
Column U : Abundance: F4: NCIM1228 grown in Avicel with Calcium, Sample 1
Column V : Abundance: F5: NCIM1228 grown in Avicel with Calcium, Sample 2
Column W : Abundance: F6: NCIM1228 grown in Avicel with Calcium, Sample 3
Column X : Abundance: F7: ∆Snf1 grown in Avicel, Sample 1
Column Y : Abundance: F8: ∆Snf1 grown in Avicel, Sample 2
Column Z : Abundance: F9: ∆Snf1 grown in Avicel, Sample 3
Column AA: Abundance: F10: ∆Snf1 grown in Avicel with Calcium, Sample 1
Column AB: Abundance: F11: ∆Snf1 grown in Avicel with Calcium, Sample 2
Column AC: Abundance: F12: ∆Snf1 grown in Avicel with Calcium, Sample 3
Column AD: Found in Sample: F1: Abundance peak status in NCIM Avicel Sample1
Column AE: Found in Sample: F2: Abundance peak status in NCIM Avicel Sample2
Column AF: Found in Sample: F3: Abundance peak status in NCIM Avicel Sample3
Column AG: Found in Sample: F4: Abundance peak status NCIM Avi+Ca2+ Sample1
Column AH: Found in Sample: F5: Abundance peak status NCIM Avi+Ca2+ Sample2
Column AI: Found in Sample: F6: Abundance peak status NCIM Avi+Ca2+ Sample3
Column AJ: Found in Sample: F7: Abundance peak status ∆Snf1 Avicel Sample1
Column AK: Found in Sample: F8: Abundance peak status ∆Snf1 Avicel Sample2
Column AL: Found in Sample: F9: Abundance peak status ∆Snf1 Avicel Sample3
Column AM: Found in Sample: F10: Abundance peak status ∆Snf1 Avi+Ca2+ Sample1
Column AN: Found in Sample: F11: Abundance peak status ∆Snf1 Avi+Ca2+ Sample2
Column AO: Found in Sample: F12: Abundance peak status ∆Snf1 Avi+Ca2+ Sample3
Column AP: # Protein Groups
Column AQ: Any post-translational Modifications detected on the protein
The hidden rows (orange)represents the peptides identified for the protein represented in the preceding row. The first row in every hidden raw group represents the title of the columns of the hidden rows which are as follows:
Column A : Empty
Column B : Checked
Column C : Confidence
Column D : Annotated Sequence
Column E : Modifications
Column F : Contaminant
Column G : Qvality PEP
Column H : Qvality q-value
Column I : # Protein Groups
Column J : # Protein
Column K : # PSMs
Column L : Master Protein Accessions
Column M : Positions in Master Proteins
Column N : Modifications in Master Proteins
Column O : # Missed Cleavages
Column P : Theo. MH+ [Da]
Column Q : Abundances (Scaled)
Column R : Found in F1: NCIM1228 grown in Avicel, Sample 1
Column S : Found in F2: NCIM1228 grown in Avicel, Sample 2
Column T : Found in F3: NCIM1228 grown in Avicel, Sample 3
Column U : Found in F4: NCIM1228 grown in Avicel with Calcium, Sample 1
Column V : Found in F5: NCIM1228 grown in Avicel with Calcium, Sample 2
Column W : Found in F6: NCIM1228 grown in Avicel with Calcium, Sample 3
Column X : Found in F7: ∆Snf1 grown in Avicel, Sample 1
Column Y : Found in F8: ∆Snf1 grown in Avicel, Sample 2
Column Z : Found in F9: ∆Snf1 grown in Avicel, Sample 3
Column AA: Found in F10: ∆Snf1 grown in Avicel with Calcium, Sample 1
Column AB: Found in F11: ∆Snf1 grown in Avicel with Calcium, Sample 2
Column AC: Found in F12: ∆Snf1 grown in Avicel with Calcium, Sample 3
Column AD: Confidence (by Search Engine): Sequest HT
Column AE: Percolator q-Value (by Search Engine) ): Sequest HT
Column AF: Percolator PEP (by Search Engine): Sequest HT
Column AG: XCorr (by Search Engine): Sequest HT
Column AH: Top Apex RT [min]
The hidden rows (grey)represents the details of peptides identified for the protein represented in the preceding row. The first row in every hidden row group represents the title of the columns of the hidden rows which are as follows:
Column C: Protein FDR Confidence: Combined
Column D: Accession
Column E: Description
Column F: Sequence
Column G: Exp. q-value: Combined
Column H: Contaminant
Column I: Sum PEP Score
Column J: Coverage [%]
Column K: # Peptides
Column L: # PSMs
Column M: # Unique Peptides
Column N: # AAs
Column O: MW [kDa]
Column P: calc. pI
Column Q: Score Sequest HT: Sequest HT
Column R: Abundances (Normalized): F11: Sample
Column S: Abundances (Normalized): F12: Sample
Column T: Abundance: F1: Sample
Column U: Abundance: F2: Sample
Column V: Abundance: F3: Sample
Column W: Abundance: F4: Sample
Column X: Abundance: F5: Sample
Column Y: Abundance: F6: Sample
Column Z: Abundance: F7: Sample
Column AA: Abundance: F8: Sample
Column AB: Abundance: F9: Sample
Column AC: Abundance: F10: Sample
Column AD: Abundance: F11: Sample
Column AE: Abundance: F12: Sample
Column AF: Found in Sample: [S1] F1: Sample
Column AG: Found in Sample: [S2] F2: Sample
Column AH: Found in Sample: [S3] F3: Sample
Column AI: Found in Sample: [S4] F4: Sample
Column AJ: Found in Sample: [S5] F5: Sample
Column AK: Found in Sample: [S6] F6: Sample
Column AL: Found in Sample: [S7] F7: Sample
Column AM: Found in Sample: [S8] F8: Sample
Column AN: Found in Sample: [S9] F9: Sample
Column AO: Found in Sample: [S10] F10: Sample
Column AP: Found in Sample: [S11] F11: Sample
Column AQ: Found in Sample: [S12] F12: Sample
Column AR: # Protein Groups
Column AS: Modifications
Sharing/Access information
We selected all the proteins represented by at least two peptides across all the samples (in one condition) Differential abundance of protein was calculated from Log2 Fold change in Avicel+ Calcium with respect to Avicel by comparing the abundance values in a given strain. Significance of the Log2 fold change was determined by the P-value (<0.05).
Code/Software
The .RAW files were processed using Proteome DiscovererTM (Version 2.4.1.15) with Mascot and Sequest HT search engines, searching against in-house predicted proteins or draft genome database (11,213 target sequences) of P. funiculosum, Apo-1 protein sequence (Sigma), and Proteome DiscovererTM contaminant database.
Methods
Profiling of the total proteome of NCM1228 and ∆Ampk was performed under calcium-limited and calcium-replete cellulosic conditions. NCIM1228 and ∆Ampk were cultured in Mandel’s medium having cellulose, or cellulose+calcium at 28˚C (120rpm) (in triplicates)(3). 10mL mycelial culture was harvested after 48h, and the remaining culture was incubated for another 72h to harvest the secretome. The secretomes were examined for the desired phenotype by SDS-PAGE and enzyme assays(4, 5). Once the distinct phenotypes associated with the two strains under given conditions were ascertained, the whole cell proteome was extracted from 48h mycelial samples as previously described in Randhawa et al (2023), and quantified by the BCA method. To assess the variance during sample preparation and measurements, we added 1µg 13C and 15N labeled human Apolipoprotein (Apo-1) (Sigma) to 50µg sample before processing. The samples were alkylated and reduced before proteolytic digestion with trypsin (1µg/50µg of protein) for 16h at 37˚C(6). Peptides were purified and concentrated by C18 spin columns (ThermoFisher Scientific). Purified samples were vacuum-dried and reconstituted in 0.1%(v/v) formic acid before proceeding for LC-MS/MS analysis using ThermoFisher Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer equipped with nano-LC Easy 1200.