LC Gradient Testing Study with RM 8321, E. coli digest, and HeLa digest

Description

It may be possible to use a mixture of known peptides run on a linear gradient to create a model that can be used to predict an unknown LC gradient of unknown samples based on deviation from the model. Data from RM 8321 can also be used to test other de novo search algorithms since it is a known mixture of 439 peptides. This data set consists of LC-MS/MS analysis of RM 8321 on a linear gradient of five varied lengths (30 min, 60 min, 90 min, 120 min, and 240 min), which can be used for modeling or testing de novo searching. To facilitate future testing of LC gradient model performance, separate E. coli protein digest (Waters) and HeLa protein digest (Pierce) were separated on a typical two-step gradient. Specific LC gradient separations are described within and should be consulted. All separations, except ?130 min?, were run with the same data acquisition settings, and all were analyzed using a Thermo Fusion Lumos tribrid mass spectrometer running data-dependent acquisition using the orbitrap detector for both MS1 and MS2. These instrument method files are also available and named obviously.

Resources

Name Format Description Link
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.csv.sha256
5 2022-8-29_8321_30min-F003180.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.mzid.sha256
5 2022-8-29_8321_60min-F003182.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.mzid.sha256
5 2022-8-29_8321_90min-F003183.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.dat
5 2022-8-29_8321_90min-F003183.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.mzid.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.mzid.sha256
5 2022-8-29_8321_240min-F003186.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.mzid.sha256
5 2022-8-29_Ecoli_60minLinear-F003187.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.mzid.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.mzid.sha256
0 2022-8-29_HeLA_OTOT1.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1.raw
5 160min_OT_OT_HCDv1.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/160min_OT_OT_HCDv1.meth
5 240min_OT_OT_HCD.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/240min_OT_OT_HCD.meth
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/240min_OT_OT_HCD.meth.sha256
5 30min_OT_OT_HCD.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/30min_OT_OT_HCD.meth
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/30min_OT_OT_HCD.meth.sha256
5 60min_OT_OT_HCD.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/60min_OT_OT_HCD.meth
5 human8321.par https://data.nist.gov/od/ds/ark:/88434/mds2-3028/human8321.par
8 2022-8-29_8321_60min-F003182.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.csv
5 85min_Fast_OT_OT_HCD_v2-2.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/85min_Fast_OT_OT_HCD_v2-2.meth
5 90min_OT_OT_HCD.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/90min_OT_OT_HCD.meth
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/90min_OT_OT_HCD.meth.sha256
10 LC%20Gradient%20Testing%20Methods.docx https://data.nist.gov/od/ds/ark:/88434/mds2-3028/LC%20Gradient%20Testing%20Methods.docx
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/LC%20Gradient%20Testing%20Methods.docx.sha256
0 2022-8-29_8321_30min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min.raw
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min.raw.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/UP000000625_Ecoli_83333-canonical-2023_01.fasta
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/UP000005640_Human_9606-canonical-2023_01.fasta.sha256
47 439peptides.txt https://data.nist.gov/od/ds/ark:/88434/mds2-3028/439peptides.txt
5 Ecoli.par https://data.nist.gov/od/ds/ark:/88434/mds2-3028/Ecoli.par
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/Ecoli.par.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/human8321.par.sha256
8 2022-8-29_8321_30min-F003180.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.csv.sha256
8 2022-8-29_8321_90min-F003183.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.csv.sha256
8 2022-8-29_8321_120min-F003185.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.csv.sha256
8 2022-8-29_8321_240min-F003186.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.csv.sha256
5 2022-8-29_8321_30min-F003180.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.dat
8 2022-8-29_Ecoli_85min-F003181.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.csv.sha256
8 2022-8-29_Ecoli_130min-F003184.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.csv
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.csv.sha256
47 In addition to the file within this data set ('LC Gradient Testing Methods.docx') this file is a text based general description and inventory of the data set. https://data.nist.gov/od/ds/mds2-3028/3028_README.txt
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min-F003183.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/120min_OT_OT_HCD.meth.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/60min_OT_OT_HCD.meth.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/85min_Fast_OT_OT_HCD_v2-2.meth.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/UP000000625_Ecoli_83333-canonical-2023_01.fasta.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.mzid.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.csv.sha256
5 2022-8-29_HeLA_OTOT1-F003188.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.dat
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.csv.sha256
10 RM%208321%20Mascot%20Score%20Distributions.docx https://data.nist.gov/od/ds/ark:/88434/mds2-3028/RM%208321%20Mascot%20Score%20Distributions.docx
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min.mgf.sha256
5 2022-8-29_8321_60min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min.mgf
5 2022-8-29_8321_90min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min.mgf
5 2022-8-29_8321_120min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min.mgf
5 2022-8-29_Ecoli_60minLinear.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear.mgf
5 2022-8-29_Ecoli_130min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min.mgf
0 2022-8-29_Ecoli_60minLinear.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear.raw
0 2022-8-29_Ecoli_85min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min.raw
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min.raw.sha256
0 2022-8-29_Ecoli_130min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min.raw
5 2022-8-29_Ecoli_60minLinear-F003187.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.dat
5 2022-8-29_Ecoli_85min-F003181.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.dat
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/RM%208321%20Mascot%20Score%20Distributions.docx.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min.mgf.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min.mgf.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min.mgf.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear.raw.sha256
5 2022-8-29_HeLA_OTOT1.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1.mgf
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1.mgf.sha256
5 2022-8-29_8321_120min-F003185.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.dat
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min.raw.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min.raw.sha256
0 2022-8-29_8321_90min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min.raw
8 2022-8-29_Ecoli_60minLinear-F003187.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear-F003187.csv
5 2022-8-29_8321_60min-F003182.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min-F003182.dat
5 2022-8-29_8321_120min-F003185.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min-F003185.mzid
5 2022-8-29_8321_30min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min.mgf
5 2022-8-29_Ecoli_85min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min.mgf
5 120min_OT_OT_HCD.meth https://data.nist.gov/od/ds/ark:/88434/mds2-3028/120min_OT_OT_HCD.meth
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min.raw.sha256
0 2022-8-29_8321_120min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min.raw
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min.raw.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_120min.mgf.sha256
5 2022-8-29_Ecoli_130min-F003184.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.mzid.sha256
5 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/UP000005640_Human_9606-canonical-2023_01.fasta
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/439peptides.txt.sha256
8 2022-8-29_HeLA_OTOT1-F003188.csv https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.csv
5 2022-8-29_Ecoli_85min-F003181.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min-F003181.mzid
0 2022-8-29_8321_60min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_60min.raw
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_90min.mgf.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_60minLinear.mgf.sha256
5 2022-8-29_Ecoli_130min-F003184.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_130min-F003184.dat
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_30min-F003180.dat.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1.raw.sha256
0 2022-8-29_8321_240min.raw https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min.raw
5 2022-8-29_8321_240min.mgf https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min.mgf
5 2022-8-29_8321_240min-F003186.dat https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min-F003186.dat
5 2022-8-29_HeLA_OTOT1-F003188.mzid https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_HeLA_OTOT1-F003188.mzid
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/160min_OT_OT_HCDv1.meth.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_8321_240min.raw.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3028/2022-8-29_Ecoli_85min.mgf.sha256

Tags

  • lc-ms-ms
  • proteomics
  • data-dependent-acquisition
  • rm-8321

Topics

Categories