A New Software Tool for Interpretation of Accurate Mass LC/MS … · 2007. 11. 21. · Authors Beth...
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TO DOWNLOAD A COPY OF THIS POSTER, VISIT WWW.WATERS.COM/POSTERS ©2007 Waters Corporation Figure 7. Compared chromatogram view of raw LC/MS data files. INTRODUCTION Protein characterization requires efficient tools to establish a complete chemical structure. Ideally, the analysis would be sensitive to minor changes in the structure. Peptide mapping by liquid chromatography linked to high mass accuracy mass spectrometry (LC/MS) has the benefit of chemical structure identification. During protein characterization comparisons are made between batches and a control or reference standard. A software tool which makes visual and quantitative comparisons readily reported and exported can provide efficient data interpretation. We have developed prototype software to address the large data sets found in protein characterization laboratories. The peaks are detected by the Apex3D/ Peptide3D algorithms to deconvolute multiply-charged ions and combine isotopes. Apex3D and Peptide3D are specifically designed to interpret the resolved isotope clusters produced by oa-Tof mass spectrometers. The results can be viewed as a table, as a combined spectrum, or as a processed chromatogram. A New Software Tool for Interpretation of Accurate Mass LC/MS Peptide Maps Authors Beth L. Gillece-Castro, Thomas E. Wheat, Scott Berger, Marc Gorenstein, Keith Richardson, Kieran Neeson, Barry Dyson, Phillip Young, Jeff Mazzeo, and Diane Diehl Affiliations: Waters Corp., Milford, MA; Waters/Micromass MS Technologies, Wythenshaw, UK WHAT BIOPHARMALYNX DOES To provide comparative views of raw and processed data To report qualitative and quantitative differ- ences To Analyze LC/MS data from oa-Tof mass spectrometers To Match observed peptides with the sequence of the protein based on molecular weight. To identify site-specific modifications Analyte: F:\PeptideMapping_BiopharmaLynx_070622.PRO\Data\non-red-mAb_3_062007.raw Control: F:\PeptideMapping_BiopharmaLynx_070622.PRO\Data\red-mAb_1_061907.raw 6 127 Retention Time 20 40 60 80 100 120 % (max = 829607.0 Counts) -100 -75 -50 -25 0 25 50 75 100 50.9328 91.0768 87.0369 30.0108 100.6027 58.5882 64.4835 109.8121 86.0703 61.5582 28.0926 31.3116 77.5468 99.8744 44.4689 8.4277 T35 68.2229 98.3758 87.0369 91.0768 100.603 30.0108 104.804 92.9846 62.9506 28.0926 62.3174 31.3116 77.5468 99.8744 105.764 44.4689 66.9099 8.4277 T35 60.2993 Automates time consuming and tedious manual data analysis Produces annotated chromatograms, coverage maps, and tabular data Facilitates comparison between a reference standard and any number of batches or vari- ant samples Outputs include formal reports, figure cut/ paste, and tabular data export Frees users to concentrate on important ques- tions GOALS DATA REDUCTION Figure 1. 3D view of LCMS data from an oa-Tof instrument. Panel A. Full 3D view of one LC/MS analysis of a tryptic digest. Panel B. Individual isotope clusters are assigned accurate retention times, accu- rate neutral molecular weight, and summed intensity as indicated by the blue bars. Retention Time (80 min) m/z (50->1500) <-3 m in-> 850 m/z 800 A B USER CONTROLS Click to Connect Cyteine Residue Numbers Appear Detect Ions Deisotope Sum LC/MS Peptide Detection Calculate Protein Digest w/Modifications Match Chrom Table Unmatched Table PROCESSING Figure 6. Compared chromatogram view of processed LC/MS data files. Figure 9. Data table showing matched peptide peaks. Color coding makes differ- ences between samples readily visible. Figure 3. Protein Sequences can be linked by disulfide bonds. Figure 5. Data files from LC/MS oa-Tof runs can be processed from any storage device which can be browsed from the Biopharmalynx computer. Figure 2. Workflow of Biopharmalynx Data Reduction. First the LC/MS data has been peak detected, deisotoped, charge state reduced, and intensity summed. Matching occurs to calculated Figure 4. Extensive Modification List includes common antibody glycans. Control Analyte 2 BROWSER VIEWS Figure 8. Processed data in a mirror plot with differences displayed in magenta. A digest was analyzed with reduction (top) and without reduction (bottom). Significant differences between the data files are highlighted. Detailed annotation is available in the browser by pointing the cursor at individual peaks. Figure 10. Coverage Map showing results from two files, a control and an analyte. Color coding makes modifications readily visible.
Transcript of A New Software Tool for Interpretation of Accurate Mass LC/MS … · 2007. 11. 21. · Authors Beth...
TO DOWNLOAD A COPY OF THIS POSTER, VISIT WWW.WATERS.COM/POSTERS ©2007 Waters Corporation
Figure 7. Compared chromatogram view of raw LC/MS data files.
INTRODUCTION Protein characterization requires efficient tools to
establish a complete chemical structure. Ideally, the
analysis would be sensitive to minor changes in the
structure. Peptide mapping by liquid
chromatography linked to high mass accuracy mass
spectrometry (LC/MS) has the benefit of chemical
structure identification. During protein
characterization comparisons are made between
batches and a control or reference standard.
A software tool which makes visual and quantitative
comparisons readily reported and exported can
provide efficient data interpretation. We have
developed prototype software to address the large
data sets found in protein characterization
laboratories. The peaks are detected by the Apex3D/
Peptide3D algorithms to deconvolute multiply-charged
ions and combine isotopes. Apex3D and Peptide3D
are specifically designed to interpret the resolved
isotope clusters produced by oa-Tof mass
spectrometers. The results can be viewed as a table,
as a combined spectrum, or as a processed
chromatogram.
A New Software Tool for Interpretation of Accurate Mass LC/MS Peptide Maps
Authors Beth L. Gillece-Castro, Thomas E. Wheat, Scott Berger, Marc Gorenstein, Keith Richardson, Kieran Neeson, Barry Dyson, Phillip Young, Jeff Mazzeo, and Diane Diehl Affiliations: Waters Corp., Milford, MA; Waters/Micromass MS Technologies, Wythenshaw, UK
WHAT BIOPHARMALYNX DOES
To provide comparative views of raw and processed data To report qualitative and quantitative differ-
ences To Analyze LC/MS data from oa-Tof mass
spectrometers To Match observed peptides with the sequence
of the protein based on molecular weight. To identify site-specific modifications
Analyte: F:\PeptideMapping_BiopharmaLynx_070622.PRO\Data\non-red-mAb_3_062007.raw
Control: F:\PeptideMapping_BiopharmaLynx_070622.PRO\Data\red-mAb_1_061907.raw
6 127Retention Time
20 40 60 80 100 120
% (m
ax =
829
607.
0 C
ount
s)
-100
-75
-50
-25
0
25
50
75
100
50.9328
91.0768
87.036930.0108 100.6027
58.5882
64.4835109.8121
86.070361.5582
28.0926
31.3116
77.5468 99.8744
44.4689
8.4277T35 68.2229
98.3758
87.0369 91.0768
100.60330.0108
104.804
92.9846
62.950628.0926
62.317431.3116
77.546899.8744 105.76444.4689
66.90998.4277T35
60.2993
Automates time consuming and tedious manual data analysis
Produces annotated chromatograms, coverage
maps, and tabular data Facilitates comparison between a reference
standard and any number of batches or vari-ant samples
Outputs include formal reports, figure cut/
paste, and tabular data export Frees users to concentrate on important ques-
tions
GOALS
DATA REDUCTION
Figure 1. 3D view of LCMS data from an oa-Tof instrument. Panel A. Full 3D view of one LC/MS analysis of a tryptic digest. Panel B. Individual isotope clusters are assigned accurate retention times, accu-rate neutral molecular weight, and summed intensity as indicated by the blue bars.
Retention Time (80 min)
m/z
(50->
1500)
<-3
min
->
850 m/z 800
A
B
USER CONTROLS
Click to Connect Cyteine
Residue Numbers Appear
Detect Ions
Deisotope
Sum
LC/MS
Peptide Detection
Calculate Protein Digest
w/Modifications
Match Chrom
Table Unmatched Table
PROCESSING
Figure 6. Compared chromatogram view of processed LC/MS data files.
Figure 9. Data table showing matched peptide peaks. Color coding makes differ-ences between samples readily visible.
Figure 3. Protein Sequences can be linked by disulfide bonds.
Figure 5. Data files from LC/MS oa-Tof runs can be processed from any storage device which can be browsed from the Biopharmalynx computer.
Figure 2. Workflow of Biopharmalynx Data Reduction. First the LC/MS data has been peak detected, deisotoped, charge state reduced, and intensity summed. Matching occurs to calculated
Figure 4. Extensive Modification List includes common antibody glycans.
Control
Analyte 2
BROWSER VIEWS
Figure 8. Processed data in a mirror plot with differences displayed in magenta. A digest was analyzed with reduction (top) and without reduction (bottom). Significant differences between the data files are highlighted. Detailed annotation is available in the browser by pointing the cursor at individual peaks.
Figure 10. Coverage Map showing results from two files, a control and an analyte. Color coding makes modifications readily visible.
![arXiv:1808.01809v2 [math.RT] 28 Aug 2018arxiv.org/pdf/1808.01809.pdfarXiv:1808.01809v2 [math.RT] 28 Aug 2018 Gorenstein-projective and semi-Gorenstein-projective modules Claus Michael](https://static.fdocuments.net/doc/165x107/5fac03b55a4f8079e641534b/arxiv180801809v2-mathrt-28-aug-arxiv180801809v2-mathrt-28-aug-2018-gorenstein-projective.jpg)
