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Partial covariance two-dimensional mass spectrometry for bio-molecular primary structure

ABSTRACT: A new kind of two-dimensional mass spectrometry is described and applied to peptides, proteins and oligonucleotides. Partial covariance two-dimensional mass spectrometry (pC-2DMS) detects intrinsic statistical correlations between bio-molecular fragments originating from the same or consecutive decomposition events. This enables the identification of pairs of ions sharing a common origin across the entire fragment mass spectrum. The fragment-fragment correlations revealed by pC-2DMS are much more specific to the bio-molecular primary structure and its modifications than the individual fragment mass-to-charge ratios on which standard one-dimensional mass spectrometry (MS) is based. We illustrate the analytical power of pC-2DMS by demonstrating the identification of mixtures of combinatorial post-translational modification patterns inaccessible to standard MS.

INSTRUMENT(S): LTQ

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Taran Driver

LAB HEAD: Marina Edelson-Averbukh

PROVIDER: PXD010631 | Pride | 2023-09-30

REPOSITORIES: Pride

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			Action	DRS
	GSNKGAIIGLM_2__CID_NCE35.raw	Raw
	GSNKGAIIGLM_2__CID_NCE35_Centroid.raw	Raw
	GSNKGAIIGLM_2__CID_NCE35_Centroid_deisotoped.mgf	Mgf
	GSNKGAIIGLM_2__CID_NCE35_then_CID_170_9_NCE35_internal.raw	Raw
	GSNKGAIIGLM_2__CID_NCE35_then_CID_225_8_NCE35_internal.raw	Raw

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Project description:The tumoral clone of Waldenstrons macroglobulinemia (WM) shows a wide morphological heterogeneity which ranges from B-lymphocytes (BL) to plasma cells (PC). By means of genome-wide expression profiling we have been able to identify genes exclusively deregulated in BL and PC from WM, but with a similar expression pattern in their corresponding cell-counterparts from CLL and MM, as well as normal individuals. The differentially expressed genes have important functions in B-cell differentiation and oncogenesis. Thus, two of the genes down-regulated in WM-BL were IL4R, which plays a relevant role in CLL B cell survival, and BACH2 that participates in the development of class-switched PC. Interestingly, one of the up-regulated genes in WM-BL was IL6. A set of 4 genes was able to discriminate clonal B-lymphocytes from WM and CLL: LEF1 (WNT/ßcatenin pathway), MARCKS, ATXN1 and FMOD. We also found deregulation of genes involved in plasma cell differentiation such as PAX5 which was overexpressed in WM-PC, and IRF4 and BLIMP1 which were underexpressed. In addition, three of the target genes activated by PAX5 -CD79, BLNK and SYK- were up-regulated in WM-PC. In summary, these results indicate that both PC and BL from WM are genetically different from the MM and CLL cell-counterpart. Keywords: Waldenstrons macroglobulinemia, expression profiling, microarrays, Affymetrix. Bone marrow (BM) samples from 10 patients with Waldenstrons macroglobulinemia (WM), 12 with multiple myeloma (MM) and 11 with chronic lymphocytic leukemia (CLL) were included in the study. All samples corresponded to newly diagnosed untreated patients. In addition, 8 normal B lymphocytes samples (NBL) from peripheral blood and 5 normal plasma cells (NPC) from bone marrow of healthy donors were also selected in order to relate the deregulation of GEP of clonal populations to normal condition. The study was approved by the local research ethics committee and written informed consent was obtained from all patients and healthy donors.

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Partial covariance two-dimensional mass spectrometry for bio-molecular primary structure

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