Liangyi Zhang - Academia.edu (original) (raw)

Papers by Liangyi Zhang

Research paper thumbnail of Structures of α-type ions formed in the 157 nm photodissociation of singly-charged peptide ions

Journal of the American Society for Mass Spectrometry, 2006

One hundred fifty-seven nm photodissociation of singly-charged peptide ions induces the cleavage ... more One hundred fifty-seven nm photodissociation of singly-charged peptide ions induces the cleavage of ␣-carbon to carbonyl-carbon bonds along the backbone. a n ϩ 1 radical ions are observed as the primary photolysis products of peptides with N-terminal arginines in a linear ion trap mass spectrometer. The radical elimination pathways undertaken by the a n ϩ 1 radical ions to form more stable even-electron species are studied in hydrogen-deuterium (H/D) exchange experiments. Two types of a n ions along with d-type ions are observed as secondary elimination products. The relative abundance of each depends on the C-terminal residue of the radical fragment ion.

Research paper thumbnail of Radical-driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation

Journal of the American Society for Mass Spectrometry, 2009

Odd-electron a ϩ 1 radical ions generated in the 157 nm photodissociation of peptide ions were in... more Odd-electron a ϩ 1 radical ions generated in the 157 nm photodissociation of peptide ions were investigated in an ion trap mass spectrometer. To localize the radical, peptide backbone amide hydrogens were replaced with deuterium. When the resulting radical ions underwent hydrogen elimination, no H/D scrambling was obvious, suggesting that without collisional activation, the radical resides on the terminal ␣-carbon. Upon collisional excitation, oddelectron radical ions dissociate through two favored pathways: the production of a-type ions at aromatic amino acids via homolytic cleavage of backbone C ␣-C(O) bonds and side-chain losses at nonaromatic amino acids. When aromatic residues are not present, nonaromatic residues can also lead to a-type ions. In addition to a-type ions, serine and threonine yield c n-1 and a n-1 ϩ 1 ions where n denotes the position of the serine or threonine. All of these fragments appear to be directed by the radical and they strongly depend on the amino acid side-chain structure. In addition, thermal fragments are also occasionally observed following cleavage of labile Xxx-Pro bonds and their formation appears to be kinetically competitive with radical migration.

Research paper thumbnail of Use of 157-nm photodissociation to probe structures of y- and b-type ions produced in collision-induced dissociation of peptide ions

Journal of the American Society for Mass Spectrometry, 2008

y-and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptid... more y-and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptide ions are photodissociated with 157-nm light in a linear trap. y-type ions are shown to have the same structure as that of intact peptides of the same sequence with the ionizing proton located at the most basic residue(s). For generic b-type ions, the ionizing proton is shown to be sequestered at the N-terminal arginine, which is consistent with the proposed oxazolone structure.

Research paper thumbnail of Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

Journal of Proteome Research, 2009

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-offlight... more 157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-offlight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v-and w-ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as band y-type ions while glycan was primarily cleaved at glycosidic bonds.

Research paper thumbnail of De Novo Sequencing of Tryptic Peptides Derived from Deinococcus radiodurans Ribosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry

Journal of Proteome Research, 2010

Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ioniza... more Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer is used to characterize peptide mixtures derived from Deinococcus radiodurans ribosomal proteins. Tryptic peptides from 52 proteins were separated by reverse-phase liquid chromatography and spotted onto a MALDI plate. From 192 sample spots, 492 peptide ions were isolated, fragmented by both photodissociation and postsource decay (PSD), and then de novo sequenced. Three-hundred seventy-two peptides yielded sequences with 5 or more amino acids. Homology searches of these sequences against the whole bacterial proteome identified 49 ribosomal proteins, 45 of which matched with two or more peptides. Peptide de novo sequencing identified slightly more proteins than conventional database searches using Mascot and was particularly advantageous in identifying unexpected peptide modifications. In the present analysis, 52 peptide modifications were identified by de novo sequencing, most of which were not recognized by database searches.

Research paper thumbnail of Peptide Photodissociation with 157 nm Light in a Commercial Tandem Time-of-Flight Mass Spectrometer

Analytical Chemistry, 2009

Photodissociation with 157 nm light was implemented in an ABI model 4700 matrix-assisted laser de... more Photodissociation with 157 nm light was implemented in an ABI model 4700 matrix-assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer for peptide analysis. With a homemade computer program to control the light timing based on the m/z of each precursor ion, the photodissociation setup was seamlessly automated with the mass spectrometer. Peptide photodissociation in this apparatus yielded fragments similar to those observed in previous experiments with a home-built tandem-TOF mass spectrometer. Peptides having arginine at their C-termini yielded high-energy x-, v-, and w-type fragments, while peptides with Nterminal arginine produced many a-and d-type ions. Abundant immonium ions were also generated. Highquality photodissociation spectra were obtained with as little as 5 fmol of peptides. In the analysis of various tryptic peptides, photodissociation provided much more sequence information than the conventional TOF-TOF collision induced dissociation (CID). Because of the high fragmentation efficiency, sensitivity was not sacrificed to achieve this.

Research paper thumbnail of Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer

Analytical Chemistry, 2010

It has previously been shown that photodissociation of tryptic peptide ions with 157 nm light in ... more It has previously been shown that photodissociation of tryptic peptide ions with 157 nm light in a matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer generates an abundance of x-type ions. A peptide de novo sequencing algorithm has now been developed to interpret these data. By combination of photodissociation and postsource decay (PSD) spectra, the algorithm identifies x-type ions and derives peptide sequences. The confidence of amino acid assignments is evaluated by observing complementary y-, v-, and w-type ions that provide additional constraints to sequence identification. In the analysis of 31 tryptic peptides from 4 model proteins, the algorithm identified 322 (or 90.7%) of the 355 amino acids and made only 3 incorrect assignments. The other 30 amino acids were not identified because specific needed x-type ions were not detected. Based on the observation of v-and w-type ions, 45 of 50 detected leucine and isoleucine residues were successfully distinguished and there was only one mistake. The remaining four residues were not distinguished because the corresponding v-and w-type ions were not detected. These de novo sequencing results translated into successful identification of proteins through homology searches. To evaluate the robustness of the present sequencing approach, a collection of 266 tryptic peptides from 23 model proteins were analyzed and then sequenced. A total of 167 peptides yielded sequence tags of 5 or more residues. In 5 peptides, 1 or 2 residues were incorrectly assigned.

Research paper thumbnail of Structures of α-type ions formed in the 157 nm photodissociation of singly-charged peptide ions

Journal of the American Society for Mass Spectrometry, 2006

One hundred fifty-seven nm photodissociation of singly-charged peptide ions induces the cleavage ... more One hundred fifty-seven nm photodissociation of singly-charged peptide ions induces the cleavage of ␣-carbon to carbonyl-carbon bonds along the backbone. a n ϩ 1 radical ions are observed as the primary photolysis products of peptides with N-terminal arginines in a linear ion trap mass spectrometer. The radical elimination pathways undertaken by the a n ϩ 1 radical ions to form more stable even-electron species are studied in hydrogen-deuterium (H/D) exchange experiments. Two types of a n ions along with d-type ions are observed as secondary elimination products. The relative abundance of each depends on the C-terminal residue of the radical fragment ion.

Research paper thumbnail of Radical-driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation

Journal of the American Society for Mass Spectrometry, 2009

Odd-electron a ϩ 1 radical ions generated in the 157 nm photodissociation of peptide ions were in... more Odd-electron a ϩ 1 radical ions generated in the 157 nm photodissociation of peptide ions were investigated in an ion trap mass spectrometer. To localize the radical, peptide backbone amide hydrogens were replaced with deuterium. When the resulting radical ions underwent hydrogen elimination, no H/D scrambling was obvious, suggesting that without collisional activation, the radical resides on the terminal ␣-carbon. Upon collisional excitation, oddelectron radical ions dissociate through two favored pathways: the production of a-type ions at aromatic amino acids via homolytic cleavage of backbone C ␣-C(O) bonds and side-chain losses at nonaromatic amino acids. When aromatic residues are not present, nonaromatic residues can also lead to a-type ions. In addition to a-type ions, serine and threonine yield c n-1 and a n-1 ϩ 1 ions where n denotes the position of the serine or threonine. All of these fragments appear to be directed by the radical and they strongly depend on the amino acid side-chain structure. In addition, thermal fragments are also occasionally observed following cleavage of labile Xxx-Pro bonds and their formation appears to be kinetically competitive with radical migration.

Research paper thumbnail of Use of 157-nm photodissociation to probe structures of y- and b-type ions produced in collision-induced dissociation of peptide ions

Journal of the American Society for Mass Spectrometry, 2008

y-and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptid... more y-and b-type fragment ions produced in the collisional dissociation of arginine-terminated peptide ions are photodissociated with 157-nm light in a linear trap. y-type ions are shown to have the same structure as that of intact peptides of the same sequence with the ionizing proton located at the most basic residue(s). For generic b-type ions, the ionizing proton is shown to be sequestered at the N-terminal arginine, which is consistent with the proposed oxazolone structure.

Research paper thumbnail of Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

Journal of Proteome Research, 2009

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-offlight... more 157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-offlight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v-and w-ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as band y-type ions while glycan was primarily cleaved at glycosidic bonds.

Research paper thumbnail of De Novo Sequencing of Tryptic Peptides Derived from Deinococcus radiodurans Ribosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry

Journal of Proteome Research, 2010

Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ioniza... more Vacuum ultraviolet photodissociation of peptide ions in a matrix assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer is used to characterize peptide mixtures derived from Deinococcus radiodurans ribosomal proteins. Tryptic peptides from 52 proteins were separated by reverse-phase liquid chromatography and spotted onto a MALDI plate. From 192 sample spots, 492 peptide ions were isolated, fragmented by both photodissociation and postsource decay (PSD), and then de novo sequenced. Three-hundred seventy-two peptides yielded sequences with 5 or more amino acids. Homology searches of these sequences against the whole bacterial proteome identified 49 ribosomal proteins, 45 of which matched with two or more peptides. Peptide de novo sequencing identified slightly more proteins than conventional database searches using Mascot and was particularly advantageous in identifying unexpected peptide modifications. In the present analysis, 52 peptide modifications were identified by de novo sequencing, most of which were not recognized by database searches.

Research paper thumbnail of Peptide Photodissociation with 157 nm Light in a Commercial Tandem Time-of-Flight Mass Spectrometer

Analytical Chemistry, 2009

Photodissociation with 157 nm light was implemented in an ABI model 4700 matrix-assisted laser de... more Photodissociation with 157 nm light was implemented in an ABI model 4700 matrix-assisted laser desorption ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer for peptide analysis. With a homemade computer program to control the light timing based on the m/z of each precursor ion, the photodissociation setup was seamlessly automated with the mass spectrometer. Peptide photodissociation in this apparatus yielded fragments similar to those observed in previous experiments with a home-built tandem-TOF mass spectrometer. Peptides having arginine at their C-termini yielded high-energy x-, v-, and w-type fragments, while peptides with Nterminal arginine produced many a-and d-type ions. Abundant immonium ions were also generated. Highquality photodissociation spectra were obtained with as little as 5 fmol of peptides. In the analysis of various tryptic peptides, photodissociation provided much more sequence information than the conventional TOF-TOF collision induced dissociation (CID). Because of the high fragmentation efficiency, sensitivity was not sacrificed to achieve this.

Research paper thumbnail of Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer

Analytical Chemistry, 2010

It has previously been shown that photodissociation of tryptic peptide ions with 157 nm light in ... more It has previously been shown that photodissociation of tryptic peptide ions with 157 nm light in a matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight (TOF) mass spectrometer generates an abundance of x-type ions. A peptide de novo sequencing algorithm has now been developed to interpret these data. By combination of photodissociation and postsource decay (PSD) spectra, the algorithm identifies x-type ions and derives peptide sequences. The confidence of amino acid assignments is evaluated by observing complementary y-, v-, and w-type ions that provide additional constraints to sequence identification. In the analysis of 31 tryptic peptides from 4 model proteins, the algorithm identified 322 (or 90.7%) of the 355 amino acids and made only 3 incorrect assignments. The other 30 amino acids were not identified because specific needed x-type ions were not detected. Based on the observation of v-and w-type ions, 45 of 50 detected leucine and isoleucine residues were successfully distinguished and there was only one mistake. The remaining four residues were not distinguished because the corresponding v-and w-type ions were not detected. These de novo sequencing results translated into successful identification of proteins through homology searches. To evaluate the robustness of the present sequencing approach, a collection of 266 tryptic peptides from 23 model proteins were analyzed and then sequenced. A total of 167 peptides yielded sequence tags of 5 or more residues. In 5 peptides, 1 or 2 residues were incorrectly assigned.