This readme.txt file was generated on 2023-10-02 by Mohd Farid Abdul Halim Recommended citation for the data: wait for DOI ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Mass spectometry data of proteins identified in purified sample of Fdh2-Hdr complex 2. Author Information Principal Investigator Contact Information Name: Kyle Costa Institution: University of Minnesota Address: 670 Biological Sciences Center 1445 Gortner Avenue St. Paul, MN 55108 Email: kcosta@umn.edu ORCID: https://orcid.org/0000-0003-0407-1431 Associate or Co-investigator Contact Information Name: Mohd Farid Abdul Halim Institution: University of Minnesota Address: 685 Biological Sciences Center 1445 Gortner Avenue St. Paul, MN 55108 Email: faridh@umn.edu ORCID: https://orcid.org/0000-0002-2327-3621 Associate or Co-investigator Contact Information Name: Dallas Fonseca Institution: University of Minnesota Address: 685 Biological Sciences Center 1445 Gortner Avenue St. Paul, MN 55108 Email: fonse039@umn.edu ORCID: Associate or Co-investigator Contact Information Name: Thomas Niehaus Institution: University of Minnesota Address: 685 Biological Sciences Center 1445 Gortner Avenue St. Paul, MN 55108 Email: tniehaus@umn.edu ORCID: https://orcid.org/0000-0002-3575-8001 3. Date published or finalized for release: 2023-10-02 4. Date of data collection (single date, range, approximate date) : 2022-10-24 5. Geographic location of data collection (where was data collected?): University of Minnesota Center for Mass Spectrometry and Proteomics, St Paul, Minnesota, USA 6. Information about funding sources that supported the collection of the data: U.S. Department of Energy, Office of Science, Basic Energy Sciences under grant number DE-SC0019148. 7. Overview of the data (abstract): Mass spectrometry data of proteins identified from purified Fdh2-Hdr complex from Methanococcus maripaludis. The purpose of this data is part of the manuscript submission to identify the protein component of Fdh2-Hdr complex when Methanoccus mariapludis relies on Fdh2 for growh on formate as the sole electron donor. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/) 2. Links to publications that cite or use the data: Mohd Farid Abdul Halim, Dallas R Fonseca, Thomas D Niehaus, Kyle C Costa. (2023). Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. bioRxiv 2023.05.09.540023 https://doi.org/10.1101/2023.05.09.540023 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: kcosta_faridh_18801_20221024_Fdh2-Hdr-1 Short description: Raw data file of mass spectrometry analysis on purified Methanococcus maripaludis Fdh2-Hdr sample part 1. B. Filename: kcosta_faridh_18801_20221024_Fdh2-Hdr-2 Short description: Raw data file of mass spectrometry analysis on purified Methanococcus maripaludis Fdh2-Hdr sample part 2. C. Filename: kcosta_faridh_18801_20221024_correctedDatabase Short description: List of proteins identified from mass spectrometry analysis on purified Methanococcus maripaludis Fdh2-Hdr sample. 2. Relationship between files: The files contain the raw mass spectromery data of independent samples (biological replicates) and the final analysis result of matched proteins identified from the analysis. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Mass spectrometry was performed with the help of the University of Minnesota Center for Mass Spectrometry and Proteomics. A 5 µg aliquot (10ul) of each sample was made and 50 µg denaturing buffer was added to each sample (7 M urea, 2 M thiourea, 0.4 Tris pH 8, 20% acetonitrile, 10 mM TCEP, and 40 mM chloroacetamide). Samples were incubated at 37oC for 0.5 hrs. 190 µl of LC-MS grade water was added to dilute the urea. Trypsin was reconstituted in 10 mM CaCl2 (sequencing grade, Promega, Middleton, WI) and added at a 1:40 enzyme to total protein ratio. Samples were incubated for 16 hrs at 37oC. After incubation, samples were acidified to 0.3% formic acid with 10% formic acid and cleaned up with an MCX STAGE tip (39) using Empore SDB-RPS extraction disks material from 3M. The eluted samples were Speedvaced to dryness. Analytical separation and detection were performed on an UltiMate 3000 RSLCnano UHPLC system (Thermo Scientific, Waltham, MA) interfaced to an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific, San Jose, CA). All dried peptide samples were reconstituted using a load solvent mixture of 98:2, H2O:acetonitrile (ACN) with 0.1% formic acid (FA). 200 nanograms of peptide mixture in 2 µL were injected on the analytical platform equipped with a 10 µL injection loop. Chromatographic separation was performed using a self-packed C18 column (Dr. Maisch GmbH ReproSil-PUR 1.9 µm 120 Å C18aq, 100 µm ID x 45 cm length) maintained at 55 °C for the duration of the experiment. The mobile phases were (A) 0.1% FA in H2O and (B) 0.1% FA in ACN solutions. Chromatographic separation was performed using a linear gradient as follows: 5% B from 0-2.5 min, 21% B at 40 min, 35% B at 60 min, and 90% B from 62-69 min followed by a return to starting conditions. The flow rate was operated at 400 nl min-1 for 0-2 min, 315 nl min-1for 2.5-60 min, and 400 nl min-1for 62-69 min. A Nanospray Flex ion source (Thermo Fisher Scientific) was used with a source voltage of 2.1 kV and ion transfer tube temperature of 250 °C. Discovery LC-MS/MS analyses was performed using full-scan detection followed by data dependent MS2 acquisition (DDA). Full-scan detection was performed using Orbitrap detection at a resolution of 120,000, normalized automatic gain control (AGC) targeted setting of 4×105 with a 50 ms maximum ion injection time. Scan ranges of 380 m/z – 1580 m/z were used for full-scan detection. MS2 spectra were collected using a DDA design with a 3 sec cycle time in centroid mode. Fragment spectra were acquired with quadrupole isolation width of 1.6 m/z, ion trap detection, and an AGC setting of 1×104 with a 35 ms maximum injection time. The analysis of peptide fragments utilized collision induced dissociation (CID) activation at a constant collision energy of 35%, 0.25 activation Q, and 10 ms activation time. 2. Methods for processing the data: Peptide tandem MS results were searched and compiled into a protein report using Proteome Discoverer, version 2.5 (Thermo Fisher Scientific, San Jose, CA). Peptide identities were inferred through database searching using the Sequest algorithm against the Methanococcus maripaludis (strain S2 / LL) protein database (Proteome ID: UP000000590) downloaded from the online UniProtKB repository (downloaded: 2022-11-17; total protein sequences: 1,722) concatenated to a list of common laboratory protein contaminants (40). The protein database search matched trypsin-specific peptides, maximum 2 missed cleavage sites, with a precursor ion tolerance of 15 PPM and fragment ion mass tolerance of 0.6 Da. Variable peptide modifications included oxidation of methionine, pyroglutamic acid conversion from glutamine, deamidation of asparagine, acetyl and/or met-loss of the protein N-terminus. Carbamidomethylation of cysteine was specified as a fixed peptide modification. Peptide and protein identification were restricted to a 1% false discovery rate using the Percolator algorithm. 3. Instrument- or software-specific information needed to interpret the data: Thermo Proteome Discoverer 3.0.1.27 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: NA 6. Describe any quality-assurance procedures performed on the data: NA 7. People involved with sample collection, processing, analysis and/or submission: Mohd Farid Abdul Halim (Costa Lab) Todd Markowski (University of Minnesota Center for Mass Spectrometry and Proteomics) Kevin Murray (University of Minnesota Center for Mass Spectrometry and Proteomics) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: kcosta_faridh_18801_20221024_correctedDatabase ----------------------------------------- 1. Number of variables: 20 2. Number of cases/rows: 180 3. Missing data codes: The data in columns "Reactome Pathway Accession," "WikiPathway Accession," "WikiPathway description," and "Contaminant" was empty by default. 4. Variable List A. Name: Checked Description: Allows to check an item B. Name: Protein FDI Description: The level of confidence of identified protein C. Name: Description Description: The description of the protein extracted from the searched sequence database D. Name: Accession Description: The accession of the protein E. Name: Gene Symbol Description: The official gene symbol F. Name: Coverage [%] Description: The percentage of the sequence covered by identification from included search G. Name: # Peptide Description: The total number of distinct peptide sequence identified for protein H. Name: # Unique Peptide Description: The total number of distinct peptide sequence unique to the protein group I. Name: # PSMs Description: The total number of peptide-spectrum matches identified from all included searches J. Name: # PSMs Description: The total number of peptide-spectrum matches identified from all included searches K. Name: Found in Samples Description: Indicate in which samples an identification or quantifiable signal was found L. Name: Biological process Description: Protein Center GO Biological process M. Name: Cellular Component Description: Protein Center GO Cellular Component N. Name: Molecular Function Description: Protein Center GO MOlecular Function O. Name: Gene ID Description: Gene ID P. Name: Pfam IDs Description: Protein family ID Q. Name: Reactome Pathway Accession Description: Reactome Pathway Accession R. Name: WikiPathway Accession Description: WikiPathway Accession S. Name: WikiPathway Description: WikiPathway description T. Name: Contaminant Description: Contaminant