DOI: 10.5061/dryad.8gtht76wd
title: Proteome of Penicillium funiculosum NCIM1228 and ∆Snf1 grown in glucose and Avicel in the presence as well as the absence of calcium

description: 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.
description: 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 <sup>13</sup>C and
 <sup>15</sup>N 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. 
description: # 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: 1. 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. 1. Sample1.raw 2. Sample2.raw
 3. Sample3.raw 4. Sample4.raw 5. Sample5.raw 6. Sample6.raw 7. Sample7.raw
 8. Sample8.raw 9. Sample9.raw 10. Sample10.raw 11. Sample11.raw 12.
 Sample12.raw 13. 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 (&lt;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.